From 85b29b00aa23ad957802f04fff81817a144d0cda Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Mon, 3 Jan 2022 15:44:14 -0500 Subject: [PATCH] Release Candidate 2022-01-03 --- obi.owl | 49973 +++++++++++++++++++++++--------------- views/NIAID-GSC-BRC.owl | 1044 +- views/obi.obo | 3569 ++- views/obi_core.owl | 582 +- 4 files changed, 33961 insertions(+), 21207 deletions(-) diff --git a/obi.owl b/obi.owl index a0c488d4..8c1f2eb8 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2021-08-18 + 2022-01-03 @@ -188,9 +188,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -217,9 +217,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -553,10 +553,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority + relates a class of CRID to the date after which further instances should not be made, according to the central authority In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp Alan Ruttenberg - retired from use as of + retired from use as of @@ -664,9 +664,9 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 IEDB alternative term - An alternative term used by the IEDB. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB + An alternative term used by the IEDB. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB IEDB alternative term @@ -678,9 +678,9 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 FGED alternative term - An alternative term used by the Functional Genomics Data (FGED) Society. - PERSON: Chris Stoeckert, Jie Zheng - Penn Group + An alternative term used by the Functional Genomics Data (FGED) Society. + PERSON: Chris Stoeckert, Jie Zheng + Penn Group FGED alternative term @@ -955,7 +955,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - Mark Miller + Mark Miller 2018-05-11T13:47:29Z @@ -982,7 +982,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - shorthand + shorthand @@ -1260,7 +1260,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. + The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. @@ -1268,7 +1268,7 @@ c = pattern in the ink b = paper + ink r = friend - c specifically denotes r =def + c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b @@ -1284,12 +1284,12 @@ Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense + see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote + Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy - obsolete_specifically denotes + obsolete_specifically denotes true @@ -1355,9 +1355,9 @@ every c that is a concretization of g specifically denotes r - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote + see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - obsolete_materially denotes + obsolete_materially denotes true @@ -1418,7 +1418,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - obsolete_describes + obsolete_describes true @@ -1429,7 +1429,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - obsolete_represents + obsolete_represents true @@ -1572,12 +1572,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which is_supported_by_data - The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. + The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process + The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI - Philly 2011 workshop + Philly 2011 workshop is_supported_by_data @@ -1594,16 +1594,16 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has_specified_input has_specified_input - has_specified_input see is_input_of example_of_usage - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + The inverse property of is_specified_input_of + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot has_specified_input @@ -1614,12 +1614,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_concretization_of + is_concretization_of - Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. - replaced by: http://purl.obolibrary.org/obo/BFO_0000058 - PERSON: Alan Ruttenburg - PERSON: Barry Smith + Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. + replaced by: http://purl.obolibrary.org/obo/BFO_0000058 + PERSON: Alan Ruttenburg + PERSON: Barry Smith obsolete_is_concretization_of true @@ -1632,12 +1632,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_specified_input_of + is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_input_of @@ -1647,12 +1647,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_concretized_as + is_concretized_as - Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. - replaced by: http://purl.obolibrary.org/obo/BFO_0000059 - PERSON: Alan Ruttenberg - PERSON: Barry Smith + Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. + replaced by: http://purl.obolibrary.org/obo/BFO_0000059 + PERSON: Alan Ruttenberg + PERSON: Barry Smith obsolete_is_concretized_as true @@ -1664,14 +1664,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - has_quality + has_quality - A relation between an entity and a quality. For types: E has_quality Q iff: + A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm] - replaced by: http://purl.obolibrary.org/obo/BFO_0000086 - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall + replaced by: http://purl.obolibrary.org/obo/BFO_0000086 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungall obsolete_has_quality true @@ -1690,14 +1690,14 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu + has_specified_output has_specified_output - has_specified_output - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + The inverse property of is_specified_output_of PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot has_specified_output @@ -1708,15 +1708,15 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - is_realized_by - - Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] - replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall - executed_during - has_realization - is_realized_as + is_realized_by + + Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] + replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungall + executed_during + has_realization + is_realized_as obsolete_is_realized_by true @@ -1728,11 +1728,11 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - obsoleted_has_specified_output_information + obsoleted_has_specified_output_information A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data. PERSON: Alan Ruttenberg - PERSON: Frank Gibson + PERSON: Frank Gibson obsoleted_has_specified_output_information true @@ -1769,13 +1769,13 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - has_function - heart has_function to-pump-blood + has_function + heart has_function to-pump-blood - Relation between an independent continuant and a function. - replaced by: http://purl.obolibrary.org/obo/BFO_0000085 - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall + Relation between an independent continuant and a function. + replaced by: http://purl.obolibrary.org/obo/BFO_0000085 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungall obsolete_has_function true @@ -1787,7 +1787,7 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - obsoleted_is_reagent_in + obsoleted_is_reagent_in some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole @@ -1803,25 +1803,25 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - realizes - example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the + realizes + example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. - Relation between a process and a function, where the unfolding of the + Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] - replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungal - executes - has_function_part - involves_execution_of - is_realization_of + replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungal + executes + has_function_part + involves_execution_of + is_realization_of obsolete_realizes true @@ -1833,7 +1833,7 @@ instance level relation [GOC:cjm] - obsoleted_utilizes_reagent + obsoleted_utilizes_reagent see example_of_usage for is_reagent_in Relationship between a protocol application and a substance that has role reagent that participates in the protocol application @@ -1849,7 +1849,7 @@ instance level relation [GOC:cjm] - obsoleted_is_device_for + obsoleted_is_device_for some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Relationship between a device and a protocol application in which it participates @@ -1871,12 +1871,12 @@ instance level relation [GOC:cjm] + is_specified_output_of is_specified_output_of - is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_output_of @@ -1887,7 +1887,7 @@ instance level relation [GOC:cjm] - obsoleted_utilizes_device + obsoleted_utilizes_device see example_of_usage for is_device_for Relationship between protocol application and an intrument in which it participates @@ -1904,7 +1904,7 @@ instance level relation [GOC:cjm] - is_proxy_for + is_proxy_for position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. @@ -1926,12 +1926,12 @@ level of radioactivity is_proxy_for level of toxicity - has specified input information + has specified input information A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data. - PERSON: Frank Gibson + PERSON: Frank Gibson PERSON:Alan Ruttenberg - consumes data + consumes data obsoleted_has_specified_input_information true @@ -1943,12 +1943,12 @@ level of radioactivity is_proxy_for level of toxicity - has_role + has_role - A relation between a continuant C and a role R. The reciprocal relation of role_of. - replaced by: http://purl.obolibrary.org/obo/BFO_0000087 - GROUP:OBI:<http://obi.sourceforge.net> - PERSON:Chris Mungal + A relation between a continuant C and a role R. The reciprocal relation of role_of. + replaced by: http://purl.obolibrary.org/obo/BFO_0000087 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON:Chris Mungal obsolete_has_role true @@ -1960,12 +1960,12 @@ level of radioactivity is_proxy_for level of toxicity - obsolete_results_from + obsolete_results_from - 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 + 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the - obsolete_results_from + obsolete_results_from true @@ -1977,14 +1977,14 @@ level of radioactivity is_proxy_for level of toxicity - achieves_planned_objective - A cell sorting process achieves the objective specification 'material separation objective' - - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. - BP, AR, PPPB branch - PPPB branch derived - modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - achieves_planned_objective + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + achieves_planned_objective @@ -1993,14 +1993,14 @@ level of radioactivity is_proxy_for level of toxicity - is_specified_information_output_of + is_specified_information_output_of - A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. - is replaced by has_specified_output_of - PERSON: James Malone - Editor + A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. + is replaced by has_specified_output_of + PERSON: James Malone + Editor - obsoleted_is_specified_information_output_of + obsoleted_is_specified_information_output_of true @@ -2010,13 +2010,13 @@ level of radioactivity is_proxy_for level of toxicity - has grain + has grain - the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. + the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg - PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 - has grain + PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 + has grain @@ -2025,12 +2025,12 @@ level of radioactivity is_proxy_for level of toxicity - obsoleted_is_specified_information_intput_of + obsoleted_is_specified_information_intput_of - Is the inverse relation of has_specfied_input_information - is replaced by is_specified_intput_of + Is the inverse relation of has_specfied_input_information + is replaced by is_specified_intput_of - obsoleted_is_specified_information_intput_of + obsoleted_is_specified_information_intput_of true @@ -2040,7 +2040,7 @@ level of radioactivity is_proxy_for level of toxicity - is grain of + is grain of A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole. JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic. @@ -2055,13 +2055,13 @@ level of radioactivity is_proxy_for level of toxicity - provisions + provisions - A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use + A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use 5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship. - GROUP: Relations branch + GROUP: Relations branch supplies - provisions + provisions @@ -2078,14 +2078,14 @@ level of radioactivity is_proxy_for level of toxicity - has_supplier - - A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. - PERSON: Alan Rutternberg - PERSON: Cristian Cocos - PERSON: Frank Gibson - PERSON: Melanie Courtot - has_supplier + has_supplier + + A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. + PERSON: Alan Rutternberg + PERSON: Cristian Cocos + PERSON: Frank Gibson + PERSON: Melanie Courtot + has_supplier @@ -2095,12 +2095,12 @@ level of radioactivity is_proxy_for level of toxicity - objective_achieved_by + objective_achieved_by - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - objective_achieved_by + objective_achieved_by @@ -2118,17 +2118,17 @@ level of radioactivity is_proxy_for level of toxicity - is member of organization - - Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. - 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population - JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. - Person:Alan Ruttenberg - Person:Helen Parkinson - Person:Alan Ruttenberg - Person:Helen Parkinson - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - is member of organization + is member of organization + + Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. + 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population + JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. + Person:Alan Ruttenberg + Person:Helen Parkinson + Person:Alan Ruttenberg + Person:Helen Parkinson + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + is member of organization @@ -2139,10 +2139,10 @@ level of radioactivity is_proxy_for level of toxicity - has category label + has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. - has category label + has category label @@ -2153,12 +2153,12 @@ level of radioactivity is_proxy_for level of toxicity - has disposition to bind + has disposition to bind - A relationship between two material entitites that each have disposition to form a complex with the other. - This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other - IEDB - has disposition to bind + A relationship between two material entitites that each have disposition to form a complex with the other. + This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other + IEDB + has disposition to bind @@ -2177,10 +2177,10 @@ level of radioactivity is_proxy_for level of toxicity has organization member - Relating an organization to a legal person or organization. - See tracker: + Relating an organization to a legal person or organization. + See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 - Person: Jie Zheng + Person: Jie Zheng has organization member @@ -2251,13 +2251,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - process is result of - The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR + process is result of + The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR - is a relationship between a process and a preceding occurrent that directly caused the later one to occur - IEDB - PERSON:Bjoern Peters - process is result of + is a relationship between a process and a preceding occurrent that directly caused the later one to occur + IEDB + PERSON:Bjoern Peters + process is result of @@ -2266,10 +2266,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - is_described_by + is_described_by - obsolete_is_described_by + obsolete_is_described_by true @@ -2280,11 +2280,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - bound_to + bound_to A relationship between two material entities that form a complex based on a selective, non-covalent interaction. The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope. - bound_to + bound_to @@ -2503,7 +2503,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - derives from + derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) @@ -2679,7 +2679,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - surrounded by + surrounded by x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y surrounded by @@ -2816,7 +2816,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - has_feature_value + has_feature_value has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. James Malone @@ -2861,13 +2861,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ has representation 12th arrondissement of Paris - 20g + 20g I feel sick to my stomach every Tuesday 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text. Further processing may enable the value to be represented in a component data structure such as an OBI value specification. - Damion Dooley - Mark Miller + Damion Dooley + Mark Miller 2019-07-14T07:05:50Z has representation @@ -4561,14 +4561,26 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + insulin + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + + insulin + + + + - water - An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + water + An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. - water + water @@ -4577,10 +4589,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ATP - An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. + ATP + An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. - ATP + ATP @@ -4595,10 +4607,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + biotin + An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. - biotin + biotin @@ -4607,10 +4619,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + cholesterol + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. - cholesterol + cholesterol @@ -4619,10 +4631,34 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ammonia - An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. + ammonia + An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. + + ammonia + + + + + + + + + phospholipid + A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. - ammonia + phospholipid + + + + + + + + + nitrite + The nitrogen oxoanion formed by loss of a proton from nitrous acid. + + nitrite @@ -4631,10 +4667,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + carbon dioxide + A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. - carbon dioxide + carbon dioxide @@ -4643,10 +4679,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + peptide + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. - peptide + peptide @@ -4655,10 +4691,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - globulin type - One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. + globulin type + One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. - globulin type + globulin type @@ -4667,10 +4703,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - creatinine - A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. + creatinine + A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. - creatinine + creatinine @@ -4679,10 +4715,22 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + mycophenolic acid + A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. - mycophenolic acid + mycophenolic acid + + + + + + + + + creatine + A glycine derivative having methyl and amidino groups attached to the nitrogen. + + creatine @@ -4691,10 +4739,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - bilirubin IXalpha - A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. + bilirubin IXalpha + A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. - bilirubin IXalpha + bilirubin IXalpha @@ -4703,10 +4751,22 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - deoxyribonucleic acid - High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. + deoxyribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. + + deoxyribonucleic acid + + + + + + + + + progesterone + A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. - deoxyribonucleic acid + progesterone @@ -4715,9 +4775,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hydrogensulfite + hydrogensulfite - hydrogensulfite + hydrogensulfite @@ -4726,10 +4786,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - homocysteine - A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. + homocysteine + A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. - homocysteine + homocysteine @@ -4738,10 +4798,22 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glucose - An aldohexose used as a source of energy and metabolic intermediate. + glucose + An aldohexose used as a source of energy and metabolic intermediate. + + glucose + + + + + + + + + testosterone + An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. - glucose + testosterone @@ -4750,10 +4822,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + methemoglobin + A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. - methemoglobin + methemoglobin @@ -4762,10 +4834,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hydrogencarbonate - The carbon oxoanion resulting from the removal of a proton from carbonic acid. + hydrogencarbonate + The carbon oxoanion resulting from the removal of a proton from carbonic acid. - hydrogencarbonate + hydrogencarbonate @@ -4774,10 +4846,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses + cortisol + A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses - cortisol + cortisol @@ -4786,10 +4858,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 5'-adenylyl sulfate - An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. + 5'-adenylyl sulfate + An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. - 5'-adenylyl sulfate + 5'-adenylyl sulfate @@ -4798,10 +4870,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - triglyceride - Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. + triglyceride + Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. - triglyceride + triglyceride @@ -4810,10 +4882,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chloride - A halide anion formed when chlorine picks up an electron to form an an anion. + chloride + A halide anion formed when chlorine picks up an electron to form an an anion. - chloride + chloride @@ -4821,11 +4893,23 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + 3-hydroxybutyric acid + A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. + + 3-hydroxybutyric acid + + + + + + + - 3-hydroxybutyric acid - A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. + bile salt + A sodium salt of the conjugate of any bile acid with either glycine or taurine. - 3-hydroxybutyric acid + bile salt @@ -4834,11 +4918,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - molecular entity + molecular entity @@ -4847,9 +4931,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cytochalasin + cytochalasin - cytochalasin + cytochalasin + + + + + + + + + estradiol + A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. + + estradiol @@ -4858,10 +4954,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + N-ethyl-N-nitrosourea + A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. - N-ethyl-N-nitrosourea + N-ethyl-N-nitrosourea @@ -4870,10 +4966,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - proton - Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + proton + Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. - proton + proton @@ -4882,9 +4978,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - iron cation + iron cation - iron cation + iron cation @@ -4893,10 +4989,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - luciferin - A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. + luciferin + A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. - luciferin + luciferin @@ -4905,10 +5001,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - amikacin - An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. + amikacin + An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. - amikacin + amikacin @@ -4917,10 +5013,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sodium chloride - An inorganic chloride salt having sodium(1+) as the counterion. + sodium chloride + An inorganic chloride salt having sodium(1+) as the counterion. - sodium chloride + sodium chloride @@ -4929,10 +5025,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - uric acid - An oxopurine that is the final oxidation product of purine metabolism. + uric acid + An oxopurine that is the final oxidation product of purine metabolism. - uric acid + uric acid @@ -4941,9 +5037,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lead(0) + lead(0) - lead(0) + lead(0) @@ -4952,10 +5048,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + vancomycin + A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. - vancomycin + vancomycin @@ -4964,10 +5060,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + rac-lactic acid + A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. - rac-lactic acid + rac-lactic acid @@ -4976,10 +5072,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - acrylamide - A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. + acrylamide + A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. - acrylamide + acrylamide @@ -4988,10 +5084,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + dehydroepiandrosterone + An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. - dehydroepiandrosterone + dehydroepiandrosterone @@ -5000,9 +5096,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 3,3',5'-triiodothyronine + 3,3',5'-triiodothyronine - 3,3',5'-triiodothyronine + 3,3',5'-triiodothyronine @@ -5011,10 +5107,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tobramycin - A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. + tobramycin + A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. - tobramycin + tobramycin @@ -5023,10 +5119,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sodium(1+) - A monoatomic monocation obtained from sodium. + sodium(1+) + A monoatomic monocation obtained from sodium. - sodium(1+) + sodium(1+) @@ -5035,10 +5131,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - potassium(1+) - A monoatomic monocation obtained from potassium. + potassium(1+) + A monoatomic monocation obtained from potassium. - potassium(1+) + potassium(1+) @@ -5047,9 +5143,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hydroxyl + hydroxyl - hydroxyl + hydroxyl @@ -5059,10 +5155,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + deuterium atom + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). - deuterium atom + deuterium atom @@ -5071,10 +5167,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - thyroxine - An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. + thyroxine + An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. - thyroxine + thyroxine @@ -5083,9 +5179,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ruthenium atom + ruthenium atom - ruthenium atom + ruthenium atom @@ -5100,10 +5196,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fluorescein - A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. + fluorescein (lactone form) + A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. - fluorescein + fluorescein (lactone form) @@ -5112,10 +5208,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - gadodiamide hydrate - The hydrate of gadodiamide. + gadodiamide hydrate + The hydrate of gadodiamide. - gadodiamide hydrate + gadodiamide hydrate @@ -5124,10 +5220,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - gadoteridol - A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). + gadoteridol + A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). - gadoteridol + gadoteridol @@ -5136,10 +5232,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + phenol red + 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. - phenol red + phenol red @@ -5148,10 +5244,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sodium citrate dihydrate - The dihydrate of trisodium citrate. + sodium citrate dihydrate + The dihydrate of trisodium citrate. - sodium citrate dihydrate + sodium citrate dihydrate @@ -5160,10 +5256,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. + atom + A chemical entity constituting the smallest component of an element having the chemical properties of the element. - atom + atom @@ -5172,9 +5268,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - elemental oxygen + elemental oxygen - elemental oxygen + elemental oxygen @@ -5183,9 +5279,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - rare earth metal atom + rare earth metal atom - rare earth metal atom + rare earth metal atom @@ -5194,10 +5290,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - rhodium atom - A cobalt group element atom of atomic number 45. + rhodium atom + A cobalt group element atom of atomic number 45. - rhodium atom + rhodium atom @@ -5206,9 +5302,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - gadolinium atom + gadolinium atom - gadolinium atom + gadolinium atom @@ -5217,9 +5313,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - terbium atom + terbium atom - terbium atom + terbium atom @@ -5228,10 +5324,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + nucleic acid + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. - nucleic acid + nucleic acid @@ -5240,10 +5336,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ribonucleic acid - High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. + ribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. - ribonucleic acid + ribonucleic acid @@ -5252,10 +5348,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - amino acid - A carboxylic acid containing one or more amino groups. + amino acid + A carboxylic acid containing one or more amino groups. - amino acid + amino acid @@ -5264,11 +5360,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macromolecule - A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + macromolecule + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer - macromolecule + macromolecule @@ -5277,9 +5373,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hemoglobin + hemoglobin + + hemoglobin + + + + + + + + + fatty acid + Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. - hemoglobin + fatty acid @@ -5288,9 +5396,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - gadolinium molecular entity + gadolinium molecular entity - gadolinium molecular entity + gadolinium molecular entity @@ -5299,10 +5407,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - phosphate ion - A phosphorus oxoanion that is the conjugate base of phosphoric acid. + phosphate ion + A phosphorus oxoanion that is the conjugate base of phosphoric acid. - phosphate ion + phosphate ion @@ -5311,10 +5419,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - gadodiamide - A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). + gadodiamide + A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). - gadodiamide + gadodiamide @@ -5323,10 +5431,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + folic acids + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. - folic acids + folic acids @@ -5335,9 +5443,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sodium phosphate + sodium phosphate - sodium phosphate + sodium phosphate @@ -5353,10 +5461,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - phosphorus-32 atom - The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. + phosphorus-32 atom + The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. - phosphorus-32 atom + phosphorus-32 atom @@ -5372,10 +5480,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + phosphorus-33 atom + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. - phosphorus-33 atom + phosphorus-33 atom @@ -5390,9 +5498,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Cy3 dye + Cy3 dye - Cy3 dye + Cy3 dye @@ -5407,9 +5515,45 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Cy5 dye + Cy5 dye + + Cy5 dye + + + + + + + + + high-density lipoprotein + A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. They are synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport). + + high-density lipoprotein + + + + + + + + + low-density lipoprotein + A class of lipoproteins of small size (18-25 nm) and low density (1.019-1.063 g/ml) particles with a core composed mainly of cholesterol esters and smaller amounts of triglycerides. The surface monolayer consists mostly of phospholipids, a single copy of apolipoprotein B-100, and free cholesterol molecules. The main function of LDL is to transport cholesterol and cholesterol esters from the liver. Excessive levels are associated with cardiovascular disease. + + low-density lipoprotein + + + + + + + + + very-low-density lipoprotein + A class of lipoproteins of large size (30-80 nm), very low density (0.93-1.006 g/ml) particles with a core composed mainly of triglycerides and a surface monolayer of phospholipids and cholesterol into which are imbedded the apolipoproteins B, E, and C. VLDL facilitate the transport of endogenously made triglycerides to extrahepatic tissues. - Cy5 dye + very-low-density lipoprotein @@ -5418,9 +5562,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - calcium cation + calcium cation - calcium cation + calcium cation @@ -5429,10 +5573,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - magnesium cation - Any magnesium ion that is positively charged. + magnesium cation + Any magnesium ion that is positively charged. - magnesium cation + magnesium cation @@ -5440,11 +5584,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - valproic acid - A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem. + + valproic acid + A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem. - valproic acid + valproic acid @@ -5459,10 +5603,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + digoxigenin + A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. - digoxigenin + digoxigenin @@ -5471,9 +5615,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ethylenediaminetetraacetic acid + ethylenediaminetetraacetic acid - ethylenediaminetetraacetic acid + ethylenediaminetetraacetic acid @@ -5482,10 +5626,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + digoxin + A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. - digoxin + digoxin @@ -5494,9 +5638,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - double-stranded DNA + double-stranded DNA - double-stranded DNA + double-stranded DNA @@ -5505,10 +5649,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 5-bromo-2'-deoxyuridine - A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. + 5-bromo-2'-deoxyuridine + A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. - 5-bromo-2'-deoxyuridine + 5-bromo-2'-deoxyuridine @@ -5517,10 +5661,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - low-density lipoprotein cholesterol - Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). + low-density lipoprotein cholesterol + Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). - low-density lipoprotein cholesterol + low-density lipoprotein cholesterol @@ -5529,10 +5673,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - high-density lipoprotein cholesterol - Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). + high-density lipoprotein cholesterol + Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). - high-density lipoprotein cholesterol + high-density lipoprotein cholesterol @@ -5541,10 +5685,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + chromium-51 + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. - chromium-51 + chromium-51 @@ -5559,9 +5703,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Alexa Fluor 532 + Alexa Fluor 532 - Alexa Fluor 532 + Alexa Fluor 532 @@ -5576,9 +5720,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Alexa Fluor 546 + Alexa Fluor 546 - Alexa Fluor 546 + Alexa Fluor 546 @@ -5593,10 +5737,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Alexa Fluor 555 - A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. + Alexa Fluor 555 + A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. - Alexa Fluor 555 + Alexa Fluor 555 @@ -5605,10 +5749,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tritiated thymidine - Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. + tritiated thymidine + Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. - tritiated thymidine + tritiated thymidine @@ -5617,10 +5761,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - dimethyl sulfate - The dimethyl ester of sulfuric acid. + dimethyl sulfate + The dimethyl ester of sulfuric acid. - dimethyl sulfate + dimethyl sulfate @@ -5629,10 +5773,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - diethyl pyrocarbonate - The diethyl ester of dicarbonic acid. + diethyl pyrocarbonate + The diethyl ester of dicarbonic acid. - diethyl pyrocarbonate + diethyl pyrocarbonate @@ -5641,10 +5785,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 1,1-dihydroxy-3-ethoxy-2-butanone - A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. + 1,1-dihydroxy-3-ethoxy-2-butanone + A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. - 1,1-dihydroxy-3-ethoxy-2-butanone + 1,1-dihydroxy-3-ethoxy-2-butanone @@ -5653,10 +5797,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. - N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5665,10 +5809,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + N-methylisatoic anhydride + A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. - N-methylisatoic anhydride + N-methylisatoic anhydride @@ -5677,10 +5821,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + (S)-1-(4-bromoacetamidobenzyl)EDTA + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. - (S)-1-(4-bromoacetamidobenzyl)EDTA + (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5689,10 +5833,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - EDTA methidiumpropylamide - A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. + EDTA methidiumpropylamide + A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. - EDTA methidiumpropylamide + EDTA methidiumpropylamide @@ -5701,10 +5845,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + bromophenol blue + 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. - bromophenol blue + bromophenol blue @@ -5713,10 +5857,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tacrolimus hydrate - A hydrate that is the monohydrate form of tacrolimus. + tacrolimus hydrate + A hydrate that is the monohydrate form of tacrolimus. - tacrolimus hydrate + tacrolimus hydrate @@ -5725,10 +5869,22 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - oxygen radical - An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. + oxygen radical + An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. + + oxygen radical + + + + + + + + + lipoprotein + A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. - oxygen radical + lipoprotein @@ -5737,9 +5893,31 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - thyroid stimulating hormone + thyroid stimulating hormone + + thyroid stimulating hormone + + + + + + + + + Luteinizing hormone + + Luteinizing hormone + + + + + + + + + Follicle stimulating hormone - thyroid stimulating hormone + Follicle stimulating hormone @@ -5748,10 +5926,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + 25-hydroxyvitamin D2 + A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. - 25-hydroxyvitamin D2 + 25-hydroxyvitamin D2 @@ -5760,10 +5938,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + tris + A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. - tris + tris @@ -5771,13 +5949,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - Any type of microscopy where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. - FM - fluorescence imaging - fluorescence microscopic imaging - CHMO - fluorescence microscopy + + + + + + + + + + + + + + + + + + + Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. + FM + fluorescence imaging + fluorescence microscopic imaging + CHMO + fluorescence microscopy assay @@ -5786,18 +5981,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. - CLSM - LSCM - confocal fluorescence imaging - confocal laser scanning fluorescence microscopy - confocal laser scanning microscopy - confocal-laser scanning microscopy - fluorescence confocal microscopy - fluorescence confocal scanning laser microscopy - scanning confocal fluorescence microscopy - CHMO - confocal fluorescence microscopy + Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. + CLSM + LSCM + confocal fluorescence imaging + confocal laser scanning fluorescence microscopy + confocal laser scanning microscopy + confocal-laser scanning microscopy + fluorescence confocal microscopy + fluorescence confocal scanning laser microscopy + scanning confocal fluorescence microscopy + CHMO + confocal fluorescence microscopy assay @@ -5806,12 +6001,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. - OM - light microscopy - optical microscopy - CHMO - light microscopy + Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. + OM + light microscopy + optical microscopy + CHMO + light microscopy assay @@ -5820,18 +6015,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. - LC-MS-MS - LC-MS/MS - LC-MS2 - LC-MSMS - LC/MS/MS - LCMSMS - liquid chromatography tandem mass spectrometry - liquid chromatography tandem mass spectroscopy - liquid chromatography-tandem mass spectroscopy + A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. + LC-MS-MS + LC-MS/MS + LC-MS2 + LC-MSMS + LC/MS/MS + LCMSMS + liquid chromatography tandem mass spectrometry + liquid chromatography tandem mass spectroscopy + liquid chromatography-tandem mass spectroscopy CHMO - liquid chromatography-tandem mass spectrometry + liquid chromatography-tandem mass spectrometry @@ -5865,18 +6060,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + cell line cell cell line cell - cell line cell 细胞系细胞 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 - 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 + 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 + cell line cell cell line cell - cell line cell 细胞系细胞 @@ -5897,14 +6092,14 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + mortal cell line cell mortal cell line cell - mortal cell line cell 非永生细胞系细胞 A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. + mortal cell line cell mortal cell line cell - mortal cell line cell 非永生细胞系细胞 @@ -5914,15 +6109,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + immortal cell line cell immortal cell line cell - immortal cell line cell 永生细胞系细胞 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. 预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。 + immortal cell line cell immortal cell line cell - immortal cell line cell 永生细胞系细胞 @@ -5947,7 +6142,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ cell line 细胞系 A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). - A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). 一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 @@ -5976,7 +6171,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ immortal cell line - A cell line that is expected to be capable of indefinite propagation in an vitro culture. + A cell line that is expected to be capable of indefinite propagation in an vitro culture. immortal cell line @@ -6007,7 +6202,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ mortal cell line - A cell line is able to support only a limited number of passages in vitro. + A cell line is able to support only a limited number of passages in vitro. mortal cell line @@ -6018,13 +6213,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + cell cell - cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + cell cell - cell @@ -6063,10 +6258,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - primary cultured cell - A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. + primary cultured cell + A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. - primary cultured cell + primary cultured cell @@ -6075,10 +6270,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - native cell - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + native cell + A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - native cell + native cell @@ -6106,10 +6301,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cultured cell - A cell in vitro that is or has been maintained or propagated as part of a cell culture. + cultured cell + A cell in vitro that is or has been maintained or propagated as part of a cell culture. - cultured cell + cultured cell @@ -6118,10 +6313,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fibroblast - A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. + fibroblast + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. - fibroblast + fibroblast @@ -6130,10 +6325,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - epithelial cell - A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. + epithelial cell + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. - epithelial cell + epithelial cell @@ -6143,10 +6338,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mesothelial cell - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + mesothelial cell + A flattened epithelial cell of mesenchymal origin that lines the serous cavity. - mesothelial cell + mesothelial cell @@ -6155,10 +6350,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - T cell - A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. + T cell + A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. - T cell + T cell @@ -6167,10 +6362,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mast cell - A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. + mast cell + A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. - mast cell + mast cell @@ -6179,10 +6374,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hepatocyte - The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. + hepatocyte + The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. - hepatocyte + hepatocyte @@ -6191,10 +6386,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - erythrocyte - A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. + erythrocyte + A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. - erythrocyte + erythrocyte @@ -6203,10 +6398,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - platelet - A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. + platelet + A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. - platelet + platelet @@ -6215,10 +6410,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macrophage - A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. + macrophage + A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. - macrophage + macrophage @@ -6227,11 +6422,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell - A lymphocyte of B lineage that is capable of B cell mediated immunity. + B cell + A lymphocyte of B lineage that is capable of B cell mediated immunity. A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. - B cell + B cell @@ -6240,10 +6435,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - dendritic cell - A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). + dendritic cell + A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). - dendritic cell + dendritic cell @@ -6251,13 +6446,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + neuron neuron - neuron - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + neuron neuron - neuron @@ -6266,10 +6461,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lymphocyte - A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. + lymphocyte + A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - lymphocyte + lymphocyte @@ -6278,10 +6473,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - megakaryocyte - A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. + megakaryocyte + A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. - megakaryocyte + megakaryocyte @@ -6290,10 +6485,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - reticulocyte - An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. + reticulocyte + An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. - reticulocyte + reticulocyte @@ -6302,10 +6497,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - band form neutrophil - A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. + band form neutrophil + A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. - band form neutrophil + band form neutrophil @@ -6315,10 +6510,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - nucleate erythrocyte - An erythrocyte having a nucleus. + nucleate erythrocyte + An erythrocyte having a nucleus. - nucleate erythrocyte + nucleate erythrocyte @@ -6329,10 +6524,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - monocyte - Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. + monocyte + Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. - monocyte + monocyte @@ -6348,10 +6543,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - experimentally modified cell in vitro - A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. + experimentally modified cell in vitro + A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. - experimentally modified cell in vitro + experimentally modified cell in vitro @@ -6360,10 +6555,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD4-positive, alpha-beta T cell - A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. + CD4-positive, alpha-beta T cell + A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. - CD4-positive, alpha-beta T cell + CD4-positive, alpha-beta T cell @@ -6372,10 +6567,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta T cell - A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. + CD8-positive, alpha-beta T cell + A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. - CD8-positive, alpha-beta T cell + CD8-positive, alpha-beta T cell @@ -6384,10 +6579,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - leukocyte - An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. + leukocyte + An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. - leukocyte + leukocyte @@ -6396,10 +6591,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - basophil - Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. + basophil + Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. - basophil + basophil @@ -6409,10 +6604,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - eosinophil - Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. + eosinophil + Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. - eosinophil + eosinophil @@ -6422,10 +6617,22 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - neutrophil - Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. + neutrophil + Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. + + neutrophil + + + + + + + + + immature neutrophil + Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. - neutrophil + immature neutrophil @@ -6434,10 +6641,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - plasma cell - A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. + plasma cell + A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. - plasma cell + plasma cell @@ -6446,10 +6653,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - alpha-beta T cell - A T cell that expresses an alpha-beta T cell receptor complex. + alpha-beta T cell + A T cell that expresses an alpha-beta T cell receptor complex. - alpha-beta T cell + alpha-beta T cell @@ -6458,10 +6665,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta cytotoxic T cell - A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. + CD8-positive, alpha-beta cytotoxic T cell + A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. - CD8-positive, alpha-beta cytotoxic T cell + CD8-positive, alpha-beta cytotoxic T cell @@ -6470,10 +6677,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mature NK T cell - A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. + mature NK T cell + A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. - mature NK T cell + mature NK T cell @@ -6482,10 +6689,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - promyelocyte - A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. + promyelocyte + A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. - promyelocyte + promyelocyte @@ -6494,10 +6701,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mononuclear cell - A leukocyte with a single non-segmented nucleus in the mature form. + mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form. - mononuclear cell + mononuclear cell @@ -6506,10 +6713,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - metamyelocyte - A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. + metamyelocyte + A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. - metamyelocyte + metamyelocyte @@ -6518,10 +6725,22 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - myelocyte - A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. + myelocyte + A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. + + myelocyte + + + + + + + + + neural cell + A cell that is part of the nervous system. - myelocyte + neural cell @@ -6538,14 +6757,26 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + complex of molecular entities + A complex of two or more molecular entities that are not covalently bound. + + complex of molecular entities + + + + - soil - Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. + soil + Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. - soil + soil @@ -6554,10 +6785,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - podzol - Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. + podzol + Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. - podzol + podzol @@ -6566,10 +6797,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - environmental material - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. + environmental material + A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. - environmental material + environmental material @@ -6586,10 +6817,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chromatin - The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + chromatin + The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. - chromatin + chromatin @@ -6599,10 +6830,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - core promoter sequence-specific DNA binding - Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. + core promoter sequence-specific DNA binding + Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. - core promoter sequence-specific DNA binding + core promoter sequence-specific DNA binding @@ -6620,10 +6851,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - transcription, RNA-templated - The cellular synthesis of RNA on a template of RNA. + transcription, RNA-templated + The cellular synthesis of RNA on a template of RNA. - transcription, RNA-templated + transcription, RNA-templated @@ -6632,10 +6863,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - action potential - A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. + action potential + A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. - action potential + action potential @@ -6644,10 +6875,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - antibody-dependent cellular cytotoxicity - Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells. + antibody-dependent cellular cytotoxicity + Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells. - antibody-dependent cellular cytotoxicity + antibody-dependent cellular cytotoxicity @@ -6656,10 +6887,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - type IV hypersensitivity - An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. + type IV hypersensitivity + An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. - type IV hypersensitivity + type IV hypersensitivity @@ -6668,10 +6899,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cytokine production - The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + cytokine production + The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - cytokine production + cytokine production @@ -6680,10 +6911,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cell killing - Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. + cell killing + Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. - cell killing + cell killing @@ -6692,10 +6923,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - T cell mediated cytotoxicity - The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. + T cell mediated cytotoxicity + The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. - T cell mediated cytotoxicity + T cell mediated cytotoxicity @@ -6704,10 +6935,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - adaptive immune response - An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). + adaptive immune response + An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). - adaptive immune response + adaptive immune response @@ -6716,10 +6947,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cytokine production involved in immune response - The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. + cytokine production involved in immune response + The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. - cytokine production involved in immune response + cytokine production involved in immune response @@ -6737,10 +6968,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tolerance induction - A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. + tolerance induction + A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. - tolerance induction + tolerance induction @@ -6749,10 +6980,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell tolerance induction - A process involving any mechanism for tolerance induction in B cells. + B cell tolerance induction + A process involving any mechanism for tolerance induction in B cells. - B cell tolerance induction + B cell tolerance induction @@ -6761,10 +6992,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - T cell tolerance induction - A process involving any mechanism for tolerance induction in T cells. + T cell tolerance induction + A process involving any mechanism for tolerance induction in T cells. - T cell tolerance induction + T cell tolerance induction @@ -6773,10 +7004,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hypersensitivity - An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. + hypersensitivity + An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. - hypersensitivity + hypersensitivity @@ -6785,10 +7016,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cytokine production involved in inflammatory response - The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. + cytokine production involved in inflammatory response + The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. - cytokine production involved in inflammatory response + cytokine production involved in inflammatory response @@ -6797,10 +7028,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glomerular filtration - The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. + glomerular filtration + The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. - glomerular filtration + glomerular filtration @@ -6809,10 +7040,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - molecular_function - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular_function + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. - molecular_function + molecular_function @@ -6821,10 +7052,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - antigen binding - Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. + antigen binding + Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. - antigen binding + antigen binding @@ -6833,10 +7064,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - catalytic activity - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + catalytic activity + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - catalytic activity + catalytic activity @@ -6845,10 +7076,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - RNA-directed DNA polymerase activity - Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. + RNA-directed DNA polymerase activity + Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. - RNA-directed DNA polymerase activity + RNA-directed DNA polymerase activity @@ -6857,10 +7088,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - acetylcholinesterase activity - Catalysis of the reaction: acetylcholine + H2O = choline + acetate. + acetylcholinesterase activity + Catalysis of the reaction: acetylcholine + H2O = choline + acetate. - acetylcholinesterase activity + acetylcholinesterase activity @@ -6869,10 +7100,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glutathione transferase activity - Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. + glutathione transferase activity + Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. - glutathione transferase activity + glutathione transferase activity @@ -6881,10 +7112,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ion channel activity - Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). + ion channel activity + Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). - ion channel activity + ion channel activity @@ -6893,10 +7124,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cellular_component - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + cellular_component + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - cellular_component + cellular_component @@ -6905,10 +7136,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fibrinogen complex - A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. + fibrinogen complex + A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. - fibrinogen complex + fibrinogen complex @@ -6917,10 +7148,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chromosome - A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. + chromosome + A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. - chromosome + chromosome @@ -6929,10 +7160,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mitochondrion - A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. + mitochondrion + A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. - mitochondrion + mitochondrion @@ -6941,10 +7172,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glucose metabolic process - The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. + glucose metabolic process + The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. - glucose metabolic process + glucose metabolic process @@ -6953,10 +7184,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - DNA replication - The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. + DNA replication + The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. - DNA replication + DNA replication @@ -6965,10 +7196,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - DNA methylation - The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. + DNA methylation + The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. - DNA methylation + DNA methylation @@ -6977,10 +7208,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chromatin remodeling - Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. + chromatin remodeling + Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. - chromatin remodeling + chromatin remodeling @@ -6989,10 +7220,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - phagocytosis - A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. + phagocytosis + A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. - phagocytosis + phagocytosis @@ -7001,10 +7232,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immune response - Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. + immune response + Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. - immune response + immune response @@ -7013,10 +7244,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cellular response to DNA damage stimulus - Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. + cellular response to DNA damage stimulus + Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. - cellular response to DNA damage stimulus + cellular response to DNA damage stimulus @@ -7025,10 +7256,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cell cycle - The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. + cell cycle + The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. - cell cycle + cell cycle @@ -7037,10 +7268,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - blood coagulation - The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. + blood coagulation + The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. - blood coagulation + blood coagulation @@ -7050,10 +7281,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological_process + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - biological_process + biological_process @@ -7062,10 +7293,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - opsonization - The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody. + opsonization + The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody. - opsonization + opsonization @@ -7074,10 +7305,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cell population proliferation - The multiplication or reproduction of cells, resulting in the expansion of a cell population. + cell population proliferation + The multiplication or reproduction of cells, resulting in the expansion of a cell population. - cell population proliferation + cell population proliferation @@ -7086,10 +7317,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fertilization - The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). + fertilization + The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). - fertilization + fertilization @@ -7098,10 +7329,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cellular process - Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + cellular process + Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - cellular process + cellular process @@ -7110,10 +7341,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - gene expression - The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. + gene expression + The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. - gene expression + gene expression @@ -7122,10 +7353,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - vascular endothelial growth factor production - The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + vascular endothelial growth factor production + The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - vascular endothelial growth factor production + vascular endothelial growth factor production @@ -7134,10 +7365,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immunoglobulin mediated immune response - An immune response mediated by immunoglobulins, whether cell-bound or in solution. + immunoglobulin mediated immune response + An immune response mediated by immunoglobulins, whether cell-bound or in solution. - immunoglobulin mediated immune response + immunoglobulin mediated immune response @@ -7146,10 +7377,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - histone modification - The covalent alteration of one or more amino acid residues within a histone protein. + histone modification + The covalent alteration of one or more amino acid residues within a histone protein. - histone modification + histone modification @@ -7158,10 +7389,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hydrolase activity, acting on ester bonds - Catalysis of the hydrolysis of any ester bond. + hydrolase activity, acting on ester bonds + Catalysis of the hydrolysis of any ester bond. - hydrolase activity, acting on ester bonds + hydrolase activity, acting on ester bonds @@ -7170,10 +7401,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immunoglobulin complex - A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + immunoglobulin complex + A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - immunoglobulin complex + immunoglobulin complex @@ -7182,10 +7413,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell receptor complex - An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. + B cell receptor complex + An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - B cell receptor complex + B cell receptor complex @@ -7194,10 +7425,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - antigen processing and presentation - The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. + antigen processing and presentation + The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. - antigen processing and presentation + antigen processing and presentation @@ -7206,10 +7437,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - protein domain specific binding - Interacting selectively and non-covalently with a specific domain of a protein. + protein domain specific binding + Interacting selectively and non-covalently with a specific domain of a protein. - protein domain specific binding + protein domain specific binding @@ -7218,10 +7449,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - actin filament polymerization - Assembly of actin filaments by the addition of actin monomers to a filament. + actin filament polymerization + Assembly of actin filaments by the addition of actin monomers to a filament. - actin filament polymerization + actin filament polymerization @@ -7230,10 +7461,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hemopoiesis - The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. + hemopoiesis + The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. - hemopoiesis + hemopoiesis @@ -7242,10 +7473,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - connective tissue growth factor production - The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + connective tissue growth factor production + The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - connective tissue growth factor production + connective tissue growth factor production @@ -7254,10 +7485,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine production - The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria. + chemokine production + The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria. - chemokine production + chemokine production @@ -7266,10 +7497,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - granulocyte macrophage colony-stimulating factor production - The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + granulocyte macrophage colony-stimulating factor production + The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - granulocyte macrophage colony-stimulating factor production + granulocyte macrophage colony-stimulating factor production @@ -7278,10 +7509,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - hepatocyte growth factor production - The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + hepatocyte growth factor production + The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - hepatocyte growth factor production + hepatocyte growth factor production @@ -7290,10 +7521,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - type I interferon production - The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. + type I interferon production + The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. - type I interferon production + type I interferon production @@ -7302,10 +7533,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interferon-alpha production - The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interferon-alpha production + The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interferon-alpha production + interferon-alpha production @@ -7314,10 +7545,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interferon-beta production - The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interferon-beta production + The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interferon-beta production + interferon-beta production @@ -7326,10 +7557,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interferon-gamma production - The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. + interferon-gamma production + The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. - interferon-gamma production + interferon-gamma production @@ -7338,10 +7569,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-1 alpha production - The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-1 alpha production + The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-1 alpha production + interleukin-1 alpha production @@ -7350,10 +7581,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-1 beta production - The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-1 beta production + The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-1 beta production + interleukin-1 beta production @@ -7362,10 +7593,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-1 production - The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-1 production + The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-1 production + interleukin-1 production @@ -7374,10 +7605,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-10 production - The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-10 production + The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-10 production + interleukin-10 production @@ -7386,10 +7617,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-11 production - The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-11 production + The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-11 production + interleukin-11 production @@ -7398,10 +7629,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-12 production - The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-12 production + The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-12 production + interleukin-12 production @@ -7410,10 +7641,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-13 production - The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-13 production + The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-13 production + interleukin-13 production @@ -7422,10 +7653,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-14 production - The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-14 production + The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-14 production + interleukin-14 production @@ -7434,10 +7665,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-15 production - The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-15 production + The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-15 production + interleukin-15 production @@ -7446,10 +7677,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-16 production - The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-16 production + The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-16 production + interleukin-16 production @@ -7458,10 +7689,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-17 production - The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-17 production + The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-17 production + interleukin-17 production @@ -7470,10 +7701,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-18 production - The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-18 production + The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-18 production + interleukin-18 production @@ -7482,10 +7713,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-19 production - The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-19 production + The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-19 production + interleukin-19 production @@ -7494,10 +7725,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-2 production - The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-2 production + The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-2 production + interleukin-2 production @@ -7506,10 +7737,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-20 production - The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-20 production + The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-20 production + interleukin-20 production @@ -7518,10 +7749,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-21 production - The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-21 production + The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-21 production + interleukin-21 production @@ -7530,10 +7761,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-22 production - The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-22 production + The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-22 production + interleukin-22 production @@ -7542,10 +7773,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-23 production - The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-23 production + The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-23 production + interleukin-23 production @@ -7554,10 +7785,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-24 production - The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-24 production + The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-24 production + interleukin-24 production @@ -7566,10 +7797,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-25 production - The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-25 production + The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-25 production + interleukin-25 production @@ -7578,10 +7809,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-26 production - The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-26 production + The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-26 production + interleukin-26 production @@ -7590,10 +7821,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-27 production - The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-27 production + The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-27 production + interleukin-27 production @@ -7602,10 +7833,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-3 production - The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-3 production + The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-3 production + interleukin-3 production @@ -7614,10 +7845,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-4 production - The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-4 production + The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-4 production + interleukin-4 production @@ -7626,10 +7857,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-5 production - The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-5 production + The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-5 production + interleukin-5 production @@ -7638,10 +7869,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-6 production - The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-6 production + The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-6 production + interleukin-6 production @@ -7650,10 +7881,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-7 production - The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-7 production + The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-7 production + interleukin-7 production @@ -7662,10 +7893,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-8 production - The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-8 production + The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-8 production + interleukin-8 production @@ -7674,10 +7905,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-9 production - The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-9 production + The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-9 production + interleukin-9 production @@ -7686,10 +7917,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - TRAIL production - The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + TRAIL production + The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - TRAIL production + TRAIL production @@ -7698,11 +7929,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tumor necrosis factor production - The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. - TNF alpha production + tumor necrosis factor production + The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. + TNF alpha production - tumor necrosis factor production + tumor necrosis factor production @@ -7711,11 +7942,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lymphotoxin A production - The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A. - TNF beta production + lymphotoxin A production + The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A. + TNF beta production - lymphotoxin A production + lymphotoxin A production @@ -7724,10 +7955,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - transforming growth factor beta1 production - The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + transforming growth factor beta1 production + The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - transforming growth factor beta1 production + transforming growth factor beta1 production @@ -7736,10 +7967,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - transforming growth factor beta2 production - The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + transforming growth factor beta2 production + The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - transforming growth factor beta2 production + transforming growth factor beta2 production @@ -7748,10 +7979,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - transforming growth factor beta3 production - The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + transforming growth factor beta3 production + The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - transforming growth factor beta3 production + transforming growth factor beta3 production @@ -7766,12 +7997,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - protein-containing complex + protein-containing complex A ribosome is a protein complex. - A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein complex - protein-containing complex + protein-containing complex @@ -7780,10 +8011,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macromolecule localization - Any process in which a macromolecule is transported to, or maintained in, a specific location. + macromolecule localization + Any process in which a macromolecule is transported to, or maintained in, a specific location. - macromolecule localization + macromolecule localization @@ -7792,10 +8023,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - DNA polymerase activity - Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. + DNA polymerase activity + Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. - DNA polymerase activity + DNA polymerase activity @@ -7804,10 +8035,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - type III interferon production - The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far. + type III interferon production + The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far. - type III interferon production + type III interferon production @@ -7816,10 +8047,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-X-C motif) ligand 9 production - The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-X-C motif) ligand 9 production + The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-X-C motif) ligand 9 production + chemokine (C-X-C motif) ligand 9 production @@ -7828,10 +8059,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - helper T cell enhancement of adaptive immune response - Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell. + helper T cell enhancement of adaptive immune response + Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell. - helper T cell enhancement of adaptive immune response + helper T cell enhancement of adaptive immune response @@ -7840,10 +8071,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - helper T cell enhancement of T cell mediated immune response - Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell. + helper T cell enhancement of T cell mediated immune response + Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell. - helper T cell enhancement of T cell mediated immune response + helper T cell enhancement of T cell mediated immune response @@ -7852,10 +8083,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - helper T cell enhancement of B cell mediated immune response - Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell. + helper T cell enhancement of B cell mediated immune response + Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell. - helper T cell enhancement of B cell mediated immune response + helper T cell enhancement of B cell mediated immune response @@ -7864,10 +8095,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - granzyme A production - The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + granzyme A production + The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - granzyme A production + granzyme A production @@ -7876,10 +8107,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - perforin production - The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + perforin production + The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - perforin production + perforin production @@ -7888,10 +8119,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - granulysin production - The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + granulysin production + The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - granulysin production + granulysin production @@ -7900,10 +8131,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 20 production - The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 20 production + The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 20 production + chemokine (C-C motif) ligand 20 production @@ -7912,10 +8143,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - regulation of gene expression, epigenetic - Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. + regulation of gene expression, epigenetic + Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. - regulation of gene expression, epigenetic + regulation of gene expression, epigenetic @@ -7924,10 +8155,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - regulation of molecular function, epigenetic - Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. + regulation of molecular function, epigenetic + Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya. - regulation of molecular function, epigenetic + regulation of molecular function, epigenetic @@ -7936,10 +8167,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - T cell proliferation - The expansion of a T cell population by cell division. Follows T cell activation. + T cell proliferation + The expansion of a T cell population by cell division. Follows T cell activation. - T cell proliferation + T cell proliferation @@ -7948,10 +8179,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - T cell receptor complex - A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. + T cell receptor complex + A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. - T cell receptor complex + T cell receptor complex @@ -7960,10 +8191,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - T cell activation - The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. + T cell activation + The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. - T cell activation + T cell activation @@ -7973,12 +8204,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immunoglobulin complex, circulating - An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. - antibody + immunoglobulin complex, circulating + An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. + antibody - antibody - immunoglobulin complex, circulating + antibody + immunoglobulin complex, circulating @@ -7999,10 +8230,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - DNA polymerase complex - A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. + DNA polymerase complex + A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. - DNA polymerase complex + DNA polymerase complex @@ -8011,10 +8242,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - peptide antigen binding - Interacting selectively and non-covalently with an antigen peptide. + peptide antigen binding + Interacting selectively and non-covalently with an antigen peptide. - peptide antigen binding + peptide antigen binding @@ -8023,10 +8254,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - MHC protein complex - A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. + MHC protein complex + A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. - MHC protein complex + MHC protein complex @@ -8035,10 +8266,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - membrane-bounded organelle - Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + membrane-bounded organelle + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. - membrane-bounded organelle + membrane-bounded organelle @@ -8047,10 +8278,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cytotoxic T cell degranulation - The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. + cytotoxic T cell degranulation + The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. - cytotoxic T cell degranulation + cytotoxic T cell degranulation @@ -8059,10 +8290,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sequence-specific DNA binding - Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. + sequence-specific DNA binding + Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. - sequence-specific DNA binding + sequence-specific DNA binding @@ -8071,10 +8302,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - regulation of DNA methylation - Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. + regulation of DNA methylation + Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. - regulation of DNA methylation + regulation of DNA methylation @@ -8083,10 +8314,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macrophage migration inhibitory factor production - The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + macrophage migration inhibitory factor production + The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - macrophage migration inhibitory factor production + macrophage migration inhibitory factor production @@ -8095,10 +8326,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - oncostatin M production - The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + oncostatin M production + The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - oncostatin M production + oncostatin M production @@ -8107,10 +8338,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 17 production - The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 17 production + The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 17 production + chemokine (C-C motif) ligand 17 production @@ -8119,10 +8350,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cellular developmental process - A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. + cellular developmental process + A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. - cellular developmental process + cellular developmental process @@ -8131,10 +8362,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - response to stimulus - Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. + response to stimulus + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - response to stimulus + response to stimulus @@ -8143,10 +8374,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chromosome organization - A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. + chromosome organization + A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. - chromosome organization + chromosome organization @@ -8155,10 +8386,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - carboxylic ester hydrolase activity - Catalysis of the hydrolysis of a carboxylic ester bond. + carboxylic ester hydrolase activity + Catalysis of the hydrolysis of a carboxylic ester bond. - carboxylic ester hydrolase activity + carboxylic ester hydrolase activity @@ -8167,10 +8398,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ferritin complex - A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain. + ferritin complex + A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain. - ferritin complex + ferritin complex @@ -8179,10 +8410,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - actin polymerization-dependent cell motility - A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. + actin polymerization-dependent cell motility + A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. - actin polymerization-dependent cell motility + actin polymerization-dependent cell motility @@ -8191,10 +8422,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - transforming growth factor beta production - The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3. + transforming growth factor beta production + The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3. - transforming growth factor beta production + transforming growth factor beta production @@ -8203,10 +8434,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - monocyte chemotactic protein-1 production - The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + monocyte chemotactic protein-1 production + The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - monocyte chemotactic protein-1 production + monocyte chemotactic protein-1 production @@ -8215,10 +8446,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 4 production - The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 4 production + The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 4 production + chemokine (C-C motif) ligand 4 production @@ -8227,10 +8458,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macrophage inflammatory protein-1 gamma production - The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + macrophage inflammatory protein-1 gamma production + The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - macrophage inflammatory protein-1 gamma production + macrophage inflammatory protein-1 gamma production @@ -8239,10 +8470,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macrophage inflammatory protein-1 alpha production - The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + macrophage inflammatory protein-1 alpha production + The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - macrophage inflammatory protein-1 alpha production + macrophage inflammatory protein-1 alpha production @@ -8251,10 +8482,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 5 production - The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 5 production + The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 5 production + chemokine (C-C motif) ligand 5 production @@ -8263,10 +8494,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 1 production - The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 1 production + The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 1 production + chemokine (C-C motif) ligand 1 production @@ -8275,10 +8506,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - granulocyte colony-stimulating factor production - The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + granulocyte colony-stimulating factor production + The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - granulocyte colony-stimulating factor production + granulocyte colony-stimulating factor production @@ -8287,10 +8518,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - IP-10 production - The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + IP-10 production + The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - IP-10 production + IP-10 production @@ -8299,10 +8530,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - granzyme B production - The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + granzyme B production + The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - granzyme B production + granzyme B production @@ -8311,10 +8542,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tumor necrosis factor superfamily cytokine production - The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + tumor necrosis factor superfamily cytokine production + The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - tumor necrosis factor superfamily cytokine production + tumor necrosis factor superfamily cytokine production @@ -8323,10 +8554,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - IgG immunoglobulin complex - A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + IgG immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - IgG immunoglobulin complex + IgG immunoglobulin complex @@ -8335,10 +8566,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - IgE immunoglobulin complex - A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + IgE immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - IgE immunoglobulin complex + IgE immunoglobulin complex @@ -8347,10 +8578,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - IgA immunoglobulin complex - A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + IgA immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - IgA immunoglobulin complex + IgA immunoglobulin complex @@ -8359,10 +8590,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - IgM immunoglobulin complex - A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + IgM immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - IgM immunoglobulin complex + IgM immunoglobulin complex @@ -8371,10 +8602,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 22 production - The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 22 production + The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 22 production + chemokine (C-C motif) ligand 22 production @@ -8383,10 +8614,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - tumor necrosis factor (ligand) superfamily member 11 production - The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + tumor necrosis factor (ligand) superfamily member 11 production + The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - tumor necrosis factor (ligand) superfamily member 11 production + tumor necrosis factor (ligand) superfamily member 11 production @@ -8395,10 +8626,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-17A production - The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-17A production + The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-17A production + interleukin-17A production @@ -8407,10 +8638,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - interleukin-17F production - The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + interleukin-17F production + The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - interleukin-17F production + interleukin-17F production @@ -8419,10 +8650,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - complement-dependent cytotoxicity - Cell killing caused by the membrane attack complex formed following complement activation. + complement-dependent cytotoxicity + Cell killing caused by the membrane attack complex formed following complement activation. - complement-dependent cytotoxicity + complement-dependent cytotoxicity @@ -8431,10 +8662,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - histamine secretion mediated by immunoglobulin - Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. + histamine secretion mediated by immunoglobulin + Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. - histamine secretion mediated by immunoglobulin + histamine secretion mediated by immunoglobulin @@ -8443,10 +8674,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immune complex formation - The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. + immune complex formation + The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. - immune complex formation + immune complex formation @@ -8455,10 +8686,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immunoglobulin-mediated neutralization - The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. + immunoglobulin-mediated neutralization + The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. - immunoglobulin-mediated neutralization + immunoglobulin-mediated neutralization @@ -8467,10 +8698,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 19 production - The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 19 production + The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 19 production + chemokine (C-C motif) ligand 19 production @@ -8479,10 +8710,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-C motif) ligand 21 production - The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-C motif) ligand 21 production + The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-C motif) ligand 21 production + chemokine (C-C motif) ligand 21 production @@ -8491,10 +8722,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-X-C motif) ligand 12 production - The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-X-C motif) ligand 12 production + The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-X-C motif) ligand 12 production + chemokine (C-X-C motif) ligand 12 production @@ -8503,10 +8734,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-X-C motif) ligand 13 production - The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-X-C motif) ligand 13 production + The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-X-C motif) ligand 13 production + chemokine (C-X-C motif) ligand 13 production @@ -8515,10 +8746,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - chemokine (C-X-C motif) ligand 16 production - The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + chemokine (C-X-C motif) ligand 16 production + The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. - chemokine (C-X-C motif) ligand 16 production + chemokine (C-X-C motif) ligand 16 production @@ -8527,10 +8758,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Insulin resistance - Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. + Insulin resistance + Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. - Insulin resistance + Insulin resistance @@ -8631,7 +8862,7 @@ of this, different, term. - obsolete_artifact + obsolete_artifact true @@ -8682,7 +8913,7 @@ interpreted by or directly executed by a processing unit. Superclass was 'digitial quality' person:Chris Stoeckert - OBI_0000261 + OBI_0000261 group:OBI obsolete2_digital entity @@ -8755,7 +8986,7 @@ Superclass was 'digitial quality' - obsolete_material_entity + obsolete_material_entity true @@ -8772,7 +9003,7 @@ Superclass was 'digitial quality' Superclass was 'digital entity' digital_entity person:Chris Stoeckert - OBI_0000244 + OBI_0000244 group:OBI obsolete2_binary digital entity @@ -8785,12 +9016,12 @@ Superclass was 'digital entity' - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy + The length of a ruler. + a unit of measure is the quality of some material entity compared to which another quality is some multiple of. + Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy - obsolete_unit of measure + obsolete_unit of measure true @@ -8989,15 +9220,15 @@ this case we explicitly refer to the singular form obsolete_study interpretation A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter - PERSON: Alan Ruttenberg + PERSON: Alan Ruttenberg PERSON: Jennifer Fostel - PERSON: Melanie Courtot - conclusion - OBI_0000005 + PERSON: Melanie Courtot + conclusion + OBI_0000005 obsolete_study interpretation true @@ -9050,8 +9281,8 @@ this case we explicitly refer to the singular form superclass was 'digital document' digital_entity person:Chris Stoeckert - OBI_0000132 - group:OBI + OBI_0000132 + group:OBI obsolete2_text based digital entity true @@ -9104,7 +9335,7 @@ superclass was 'digital document' Replaced by defined version of figure person:Alan Ruttenberg person:Allyson Lister - OBI_0000027 + OBI_0000027 group:OBI obsolete2_report figure @@ -9231,17 +9462,17 @@ whole sentence is deleted. report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure + 2009-03-16: needs some more work (clarify relations). + 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion + Replaced by textual entity and figure There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg PERSON: Allyson Lister - PERSON: Melanie Courtot + PERSON: Melanie Courtot GROUP:OBI - OBI_0000001 + OBI_0000001 obsolete_report element true @@ -9258,7 +9489,7 @@ whole sentence is deleted. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' person:Jennifer Fostel - OBI_0000222 + OBI_0000222 group:OBI obsolete2_binary executable @@ -9291,10 +9522,10 @@ superclass was 'digital entity' report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion person:Alan Ruttenberg person:Allyson Lister - OBI_0000265 + OBI_0000265 group:OBI obsolete_report table @@ -9418,7 +9649,7 @@ Request that IAO either clarify these or change definitions not to use them3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' person:Jennifer Fostel - OBI_0000195 + OBI_0000195 group:OBI obsolete2_digital document @@ -9455,11 +9686,11 @@ superclass was 'digial entity' - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. + _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - obsolete_identifier + obsolete_identifier true @@ -9530,9 +9761,9 @@ Cons sometimes specifies a quality which is not a realizable. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. + Need to rework digital entity. Digital quality was suggested by Barry. - obsolete_digital quality + obsolete_digital quality true @@ -10750,10 +10981,10 @@ points together with a line. - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. + a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - obsolete_establishing a CRID registry + obsolete_establishing a CRID registry true @@ -12235,11 +12466,11 @@ No imports - Mus musculus - house mouse - mouse + Mus musculus + house mouse + mouse - Mus musculus + Mus musculus @@ -12248,13 +12479,13 @@ No imports - Rattus norvegicus - Norway rat - brown rat - rat - rats + Rattus norvegicus + Norway rat + brown rat + rat + rats - Rattus norvegicus + Rattus norvegicus @@ -12263,9 +12494,9 @@ No imports - Viruses + Viruses - Viruses + Viruses @@ -12274,9 +12505,9 @@ No imports - Herpesviridae + Herpesviridae - Herpesviridae + Herpesviridae @@ -12285,9 +12516,9 @@ No imports - Cytomegalovirus + Cytomegalovirus - Cytomegalovirus + Cytomegalovirus @@ -12296,14 +12527,14 @@ No imports - Human gammaherpesvirus 4 - Epstein Barr virus - Epstein-Barr virus - Epstein-Barr virus EBV - Human herpesvirus 4 - Human herpesvirus type 4 + Human gammaherpesvirus 4 + Epstein Barr virus + Epstein-Barr virus + Epstein-Barr virus EBV + Human herpesvirus 4 + Human herpesvirus type 4 - Human gammaherpesvirus 4 + Human gammaherpesvirus 4 @@ -12312,14 +12543,14 @@ No imports - Hepatitis B virus - Human hepatitis B virus - hepatitis B virus (HBV) - hepatitis B virus HBV - hepatitis B virus, HBV - human hepatitis B virus HBV + Hepatitis B virus + Human hepatitis B virus + hepatitis B virus (HBV) + hepatitis B virus HBV + hepatitis B virus, HBV + human hepatitis B virus HBV - Hepatitis B virus + Hepatitis B virus @@ -12328,15 +12559,15 @@ No imports - Hepacivirus C - Hepatitis C virus - hepatitis C virus HCV - human hepatitis C virus - human hepatitis C virus HCV - human hepatitis virus C HCV - post-transfusion hepatitis non A non B virus + Hepacivirus C + Hepatitis C virus + hepatitis C virus HCV + human hepatitis C virus + human hepatitis C virus HCV + human hepatitis virus C HCV + post-transfusion hepatitis non A non B virus - Hepacivirus C + Hepacivirus C @@ -12345,10 +12576,10 @@ No imports - Lentivirus - Lentivirinae + Lentivirus + Lentivirinae - Lentivirus + Lentivirus @@ -12357,17 +12588,17 @@ No imports - Human immunodeficiency virus 1 - human immunodeficiency virus 1 HIV-1 - human immunodeficiency virus HIV-1 - human immunodeficiency virus type 1 HIV 1 - human immunodeficiency virus type 1 HIV1 - human immunodeficiency virus type 1, HIV-1 - human immunodeficiency virus type I HIV-1 - human immunodeficiency virus type-1 HIV-1 - human immunodeficiency virus-1 HIV-1 + Human immunodeficiency virus 1 + human immunodeficiency virus 1 HIV-1 + human immunodeficiency virus HIV-1 + human immunodeficiency virus type 1 HIV 1 + human immunodeficiency virus type 1 HIV1 + human immunodeficiency virus type 1, HIV-1 + human immunodeficiency virus type I HIV-1 + human immunodeficiency virus type-1 HIV-1 + human immunodeficiency virus-1 HIV-1 - Human immunodeficiency virus 1 + Human immunodeficiency virus 1 @@ -12376,14 +12607,14 @@ No imports - Human immunodeficiency virus 2 - HIV type 2 - Human immunodeficiency virus type 2 - Human immunodeficiency virus-2 - human immunodeficiency virus type 2 HIV-2 - human immunodeficiency virus type 2, HIV-2 + Human immunodeficiency virus 2 + HIV type 2 + Human immunodeficiency virus type 2 + Human immunodeficiency virus-2 + human immunodeficiency virus type 2 HIV-2 + human immunodeficiency virus type 2, HIV-2 - Human immunodeficiency virus 2 + Human immunodeficiency virus 2 @@ -12392,10 +12623,10 @@ No imports - Euteleostomi - bony vertebrates + Euteleostomi + bony vertebrates - Euteleostomi + Euteleostomi @@ -12404,9 +12635,9 @@ No imports - Ecdysozoa + Ecdysozoa - Ecdysozoa + Ecdysozoa @@ -12415,9 +12646,9 @@ No imports - Treponema pallidum + Treponema pallidum - Treponema pallidum + Treponema pallidum @@ -12426,9 +12657,9 @@ No imports - Pancrustacea + Pancrustacea - Pancrustacea + Pancrustacea @@ -12437,10 +12668,10 @@ No imports - Bacteria - eubacteria + Bacteria + eubacteria - Bacteria + Bacteria @@ -12449,9 +12680,9 @@ No imports - Archaea + Archaea - Archaea + Archaea @@ -12460,11 +12691,11 @@ No imports - Riboviria - RNA viruses - RNA viruses and viroids + Riboviria + RNA viruses + RNA viruses and viroids - Riboviria + Riboviria @@ -12473,9 +12704,9 @@ No imports - Revtraviricetes + Revtraviricetes - Revtraviricetes + Revtraviricetes @@ -12484,11 +12715,11 @@ No imports - Eukaryota - eucaryotes - eukaryotes + Eukaryota + eucaryotes + eukaryotes - Eukaryota + Eukaryota @@ -12497,9 +12728,9 @@ No imports - Euarchontoglires + Euarchontoglires - Euarchontoglires + Euarchontoglires @@ -12508,10 +12739,10 @@ No imports - Tetrapoda - tetrapods + Tetrapoda + tetrapods - Tetrapoda + Tetrapoda @@ -12520,10 +12751,10 @@ No imports - Amniota - amniotes + Amniota + amniotes - Amniota + Amniota @@ -12532,9 +12763,9 @@ No imports - Opisthokonta + Opisthokonta - Opisthokonta + Opisthokonta @@ -12543,9 +12774,9 @@ No imports - Bilateria + Bilateria - Bilateria + Bilateria @@ -12554,12 +12785,12 @@ No imports - Arabidopsis thaliana - mouse-ear cress - thale cress - thale-cress + Arabidopsis thaliana + mouse-ear cress + thale cress + thale-cress - Arabidopsis thaliana + Arabidopsis thaliana @@ -12568,9 +12799,9 @@ No imports - HIV-1 group O + HIV-1 group O - HIV-1 group O + HIV-1 group O @@ -12579,9 +12810,9 @@ No imports - Murinae + Murinae - Murinae + Murinae @@ -12590,10 +12821,10 @@ No imports - Mammalia - mammals + Mammalia + mammals - Mammalia + Mammalia @@ -12602,9 +12833,9 @@ No imports - Dictyostelium discoideum + Dictyostelium discoideum - Dictyostelium discoideum + Dictyostelium discoideum @@ -12613,11 +12844,11 @@ No imports - Ascomycota - ascomycetes - sac fungi + Ascomycota + ascomycetes + sac fungi - Ascomycota + Ascomycota @@ -12626,10 +12857,10 @@ No imports - Schizosaccharomyces pombe - fission yeast + Schizosaccharomyces pombe + fission yeast - Schizosaccharomyces pombe + Schizosaccharomyces pombe @@ -12638,12 +12869,12 @@ No imports - Saccharomyces cerevisiae - S. cerevisiae - baker's yeast - brewer's yeast + Saccharomyces cerevisiae + S. cerevisiae + baker's yeast + brewer's yeast - Saccharomyces cerevisiae + Saccharomyces cerevisiae @@ -12652,9 +12883,9 @@ No imports - Neurospora + Neurospora - Neurospora + Neurospora @@ -12663,9 +12894,9 @@ No imports - Plasmodium + Plasmodium - Plasmodium + Plasmodium @@ -12674,10 +12905,10 @@ No imports - Caenorhabditis elegans - roundworm + Caenorhabditis elegans + roundworm - Caenorhabditis elegans + Caenorhabditis elegans @@ -12686,10 +12917,10 @@ No imports - Arthropoda - arthropods + Arthropoda + arthropods - Arthropoda + Arthropoda @@ -12698,10 +12929,34 @@ No imports - Daphnia - common water fleas + Daphnia + common water fleas + + Daphnia + + + + + + + + + Diptera + flies + + Diptera + + + + + + + + + Culicidae + mosquitos - Daphnia + Culicidae @@ -12710,9 +12965,9 @@ No imports - saccharomyceta + saccharomyceta - saccharomyceta + saccharomyceta @@ -12720,11 +12975,11 @@ No imports - - Drosophila melanogaster - fruit fly + + Drosophila melanogaster + fruit fly - Drosophila melanogaster + Drosophila melanogaster @@ -12733,11 +12988,11 @@ No imports - Vertebrata <vertebrates> - Vertebrata - vertebrates + Vertebrata <vertebrates> + Vertebrata + vertebrates - Vertebrata <vertebrates> + Vertebrata <vertebrates> @@ -12746,13 +13001,13 @@ No imports - Danio rerio - leopard danio - zebra danio - zebra fish - zebrafish + Danio rerio + leopard danio + zebra danio + zebra fish + zebrafish - Danio rerio + Danio rerio @@ -12761,10 +13016,10 @@ No imports - Xenopus <genus> - Xenopus + Xenopus <genus> + Xenopus - Xenopus <genus> + Xenopus <genus> @@ -12773,13 +13028,13 @@ No imports - Gallus gallus - Gallus domesticus - bantam - chicken - chickens + Gallus gallus + Gallus domesticus + bantam + chicken + chickens - Gallus gallus + Gallus gallus @@ -12788,12 +13043,12 @@ No imports - Homo sapiens - human - human being - man + Homo sapiens + human + human being + man - Homo sapiens + Homo sapiens @@ -12802,10 +13057,10 @@ No imports - Rodentia - rodent + Rodentia + rodent - Rodentia + Rodentia @@ -12814,13 +13069,13 @@ No imports - role of being consumer safety officer + role of being consumer safety officer Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm Person charged with serving as CSO, FDA official who coordinates the review - the role of a human being that is realized by enforcing regulations to ensure consumer safety + the role of a human being that is realized by enforcing regulations to ensure consumer safety Jennifer Fostel - Person:Helen Parkinson + Person:Helen Parkinson OBI, CDISC role of being consumer safety officer @@ -12835,7 +13090,7 @@ No imports A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. person:Chris Stoeckert - group:OBI + group:OBI From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. fluorescent reporter intensity @@ -12857,17 +13112,17 @@ No imports + planned process planned process - planned process - Injecting mice with a vaccine in order to test its efficacy + Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process @@ -12879,12 +13134,12 @@ objectives is a planned process. - regulator role + regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel - regulator + regulator OBI regulator role @@ -12938,14 +13193,14 @@ objectives is a planned process. - material supplier role - Jackson Labs is an organization which provide mice as experimental material + material supplier role + Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. - Supplier role is a special kind of service, e.g. biobank + Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel - material provider role - supplier + material provider role + supplier material supplier role @@ -12955,11 +13210,11 @@ objectives is a planned process. - contract research organization role + contract research organization role a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution Person: Jennifer Fostel - contract research organization + contract research organization contract research organization role @@ -12975,7 +13230,7 @@ objectives is a planned process. A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people. person:Chris Stoeckert - group:Flow Cytometry community + group:Flow Cytometry community list-mode data file @@ -12991,12 +13246,12 @@ objectives is a planned process. - classified data set + classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. - PERSON: James Malone - PERSON: Monnie McGee - data set with assigned class labels + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned class labels classified data set @@ -13012,12 +13267,12 @@ objectives is a planned process. - reference substance role + reference substance role Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. Person:Jennifer Fostel - reference substance + reference substance OBI reference substance role @@ -13028,13 +13283,13 @@ objectives is a planned process. - cytological stain role - haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin + cytological stain role + haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin - A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization - Person:Helen Parkinson + A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization + Person:Helen Parkinson Person:Jennifer Fostel - cytological stain + cytological stain cytological stain role @@ -13056,13 +13311,13 @@ objectives is a planned process. - centrifuge pellet role - Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet + centrifuge pellet role + Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. - GROUP: Role branch - OBI - 9Mar09 after discussion with process branch changed definition to include use of centrifuge; + GROUP: Role branch + OBI + 9Mar09 after discussion with process branch changed definition to include use of centrifuge; centrifuge pellet role @@ -13072,11 +13327,11 @@ objectives is a planned process. - clinical research coordinator role + clinical research coordinator role a worker role comprised of handling the administrative duties of a trial or study. Person:Jennifer Fostel - clinical research coordinator + clinical research coordinator clinical research coordinator role @@ -13098,12 +13353,12 @@ objectives is a planned process. - supernatant role - Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia + supernatant role + Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia - supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. - GROUP: Role branch - OBI + supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. + GROUP: Role branch + OBI supernatant role @@ -13135,13 +13390,13 @@ objectives is a planned process. - chromatography column + chromatography column - Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. - Frank Gibson - http://en.wikipedia.org/wiki/Column_chromatography - open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 - chromatography column + Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. + Frank Gibson + http://en.wikipedia.org/wiki/Column_chromatography + open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 + chromatography column @@ -13157,13 +13412,13 @@ objectives is a planned process. drug role - http://www.answers.com/topic/drug + http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism Role Branch - drug + drug OBI, CDISC drug role @@ -13180,13 +13435,13 @@ objectives is a planned process. - pump valve switch + pump valve switch - A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. - FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument - OBI Instrument branch - OBI - pump valve switch + A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. + FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument + OBI Instrument branch + OBI + pump valve switch @@ -13213,8 +13468,8 @@ objectives is a planned process. a book is a physical document A physical document is an object serving as a record of information by means of symbolic marks. - PERSON: Bjoern Peters - GROUP: OBI + PERSON: Bjoern Peters + GROUP: OBI physical document @@ -13291,14 +13546,14 @@ objectives is a planned process. - chromatography device + chromatography device - A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. - Frank Gibson - chromatography instrument - http://en.wikipedia.org/wiki/Chromatography - open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 - chromatography device + A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. + Frank Gibson + chromatography instrument + http://en.wikipedia.org/wiki/Chromatography + open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 + chromatography device @@ -13331,13 +13586,13 @@ objectives is a planned process. - mass spectrometer - LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific + mass spectrometer + LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific - A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum - Frank Gibson - http://en.wikipedia.org/wiki/Mass_spectrometry - mass spectrometer + A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum + Frank Gibson + http://en.wikipedia.org/wiki/Mass_spectrometry + mass spectrometer @@ -13348,9 +13603,9 @@ objectives is a planned process. obsolete_platform - A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. - OBI Instrument branch - OBI Instrument branch + A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. + OBI Instrument branch + OBI Instrument branch obsolete_platform true @@ -13387,12 +13642,12 @@ objectives is a planned process. - liquid chromatography mass spectrometry platform + liquid chromatography mass spectrometry platform - A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. - OBI instrument branch - OBI Instrument branch - liquid chromatography mass spectrometry platform + A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. + OBI instrument branch + OBI Instrument branch + liquid chromatography mass spectrometry platform @@ -13413,12 +13668,12 @@ objectives is a planned process. - microarray platform + microarray platform - A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. - OBI Instrument branch - OBI Instrument branch - microarray platform + A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. + OBI Instrument branch + OBI Instrument branch + microarray platform @@ -13433,7 +13688,7 @@ objectives is a planned process. A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role person:Chris Stoeckert person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt ratio of collected to emitted light @@ -13456,13 +13711,13 @@ objectives is a planned process. - notified body role + notified body role The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB. Person: Jennifer Fostel - notified body + notified body OBI, CDISC notified body role @@ -13493,13 +13748,13 @@ objectives is a planned process. - gamma counter - A Geiger counter + gamma counter + A Geiger counter - A processed material which measures gamma radiation - Frank Gibson - http://en.wikipedia.org/wiki/Gamma_counter - gamma counter + A processed material which measures gamma radiation + Frank Gibson + http://en.wikipedia.org/wiki/Gamma_counter + gamma counter @@ -13508,11 +13763,11 @@ objectives is a planned process. - trial monitor role + trial monitor role a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study Person:Jennifer Fostel - trial monitor + trial monitor CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study. trial monitor role @@ -13529,12 +13784,12 @@ objectives is a planned process. - positive reference substance role + positive reference substance role MMS mutagen - a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response + a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response Person: Jennifer Fostel - positive reference substance + positive reference substance positive reference substance role @@ -13594,16 +13849,16 @@ objectives is a planned process. investigation - Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation + Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived - Could add specific objective specification + Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS - study + study investigation @@ -13631,9 +13886,9 @@ editor = PRS a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") - GROUP: Role Branch - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role @@ -13643,15 +13898,15 @@ editor = PRS - reporting party role - Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. + reporting party role + Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component - MO:submitter mapped to this term. So, alternative term 'submitter' was added. + MO:submitter mapped to this term. So, alternative term 'submitter' was added. Jennifer Fostel - reporting party - submitter + reporting party + submitter OBI reporting party role @@ -13720,7 +13975,7 @@ editor = PRS assay - Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. @@ -13728,8 +13983,8 @@ editor = PRS measuring scientific observation OBI branch derived - study assay - any method + study assay + any method assay @@ -13743,7 +13998,7 @@ editor = PRS A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert - group:OBI + group:OBI quantitative confidence value @@ -13787,12 +14042,12 @@ editor = PRS - unplanned occurrence effecting an investigation + unplanned occurrence effecting an investigation Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used a process which is external in origin to the investigation that has an impact on the outcome. - PERSON: Bjoern Peters - OBI + PERSON: Bjoern Peters + OBI unplanned occurrence effecting an investigation @@ -13806,7 +14061,7 @@ editor = PRS An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel - article-without-pmid-or-doi:CDISCglossary + article-without-pmid-or-doi:CDISCglossary eMedical record @@ -13816,11 +14071,11 @@ editor = PRS - culture medium + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 - a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. - changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 + a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. + changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI @@ -13837,7 +14092,7 @@ Modification made by JZ. An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. person:Jennifer Fostel - CDISC glossary + CDISC glossary electronic case report tabulation @@ -13847,13 +14102,13 @@ Modification made by JZ. - polystyrene tube - Polystyrene tubes can be used to contain tissue culture cells during centrifgation + polystyrene tube + Polystyrene tubes can be used to contain tissue culture cells during centrifgation - A polystyrene tube is a test tube made of polystyrene - PERSON: Chris Stoeckert - PERSON: Chris Stoeckert - polystyrene tube + A polystyrene tube is a test tube made of polystyrene + PERSON: Chris Stoeckert + PERSON: Chris Stoeckert + polystyrene tube @@ -13862,14 +14117,14 @@ Modification made by JZ. - reagent role + reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush - reagent - PERSON:Matthew Brush - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + reagent + PERSON:Matthew Brush + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. @@ -13888,12 +14143,12 @@ In regard to the statement that reagents are 'distinct' from the speci - role of regulator of chemical manufacturer + role of regulator of chemical manufacturer EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture Person: Jennifer Fostel - regulator of chemical manufacture + regulator of chemical manufacture OBI role of regulator of chemical manufacturer @@ -13904,11 +14159,11 @@ In regard to the statement that reagents are 'distinct' from the speci - detector reagent role + detector reagent role - a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. - 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances - One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 + a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. + 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances + One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 detector reagent role @@ -13918,14 +14173,14 @@ In regard to the statement that reagents are 'distinct' from the speci - role of certified IRB professional + role of certified IRB professional CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional - a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA - Person:Helen Parkinson + a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA + Person:Helen Parkinson Person:Jennifer Fostel - certified IRB professional - WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional + certified IRB professional + WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional role of certified IRB professional @@ -13941,12 +14196,12 @@ In regard to the statement that reagents are 'distinct' from the speci - patient role + patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch - patient + patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role @@ -13977,15 +14232,15 @@ In regard to the statement that reagents are 'distinct' from the speci - material processing - A cell lysis, production of a cloning vector, creating a buffer. + material processing + A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca Serra + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing @@ -14017,14 +14272,14 @@ In regard to the statement that reagents are 'distinct' from the speci study subject role - Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. + Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. - A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. + A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch - OBI + OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. @@ -14043,11 +14298,11 @@ editor = PRS obsolete_role of being first subject treated - Rat 1A; first enrolled patient to receive treatment + Rat 1A; first enrolled patient to receive treatment - First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study - Role Branch - OBI + First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study + Role Branch + OBI obsolete_role of being first subject treated true @@ -14064,7 +14319,7 @@ editor = PRS A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. person:Chris Stoeckert - OBI Data Transformation branch + OBI Data Transformation branch measured expression level @@ -14074,12 +14329,12 @@ editor = PRS - responsible party role + responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel - responsible party + responsible party OBI responsible party role @@ -14090,11 +14345,11 @@ editor = PRS - principal investigator role + principal investigator role a responsible party role played by a person responsible for the overall conduct of a study Person: Jennifer Fostel - principal investigator + principal investigator CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) principal investigator role @@ -14126,12 +14381,12 @@ editor = PRS biological vector role - 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. - Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 + 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. + Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 - a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. - GROUP: Role Branch - OBI and Wikipedia + a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. + GROUP: Role Branch + OBI and Wikipedia biological vector role true @@ -14143,14 +14398,14 @@ editor = PRS - pH indicator dye role - bromophenol blue has a pH indicator dye role + pH indicator dye role + bromophenol blue has a pH indicator dye role phenol red in RPMI; pH=4 indicator dye (also carries reference role) - the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity + the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity Person: Jennifer Fostel - Person:Helen Parkinson - pH indicator dye + Person:Helen Parkinson + pH indicator dye pH indicator dye role @@ -14176,20 +14431,20 @@ editor = PRS - specimen role - liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation - 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. - GROUP: Role Branch - OBI + GROUP: Role Branch + OBI specimen role @@ -14233,13 +14488,13 @@ specimen can later be subject. - intervention design - PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. + intervention design + PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. - An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. - Philppe Rocca-Serra - OBI branch derived - intervention design + An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. + Philppe Rocca-Serra + OBI branch derived + intervention design @@ -14248,13 +14503,13 @@ specimen can later be subject. - worker role + worker role Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline - "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study + "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study Person:Jennifer Fostel - worker + worker OBI worker role @@ -14267,9 +14522,9 @@ specimen can later be subject. Bernoulli trial - An assay where the output data is a datum with one of two values denoting success and failure. - PlanAndPlannedProcess Branch - OBI branch derived + An assay where the output data is a datum with one of two values denoting success and failure. + PlanAndPlannedProcess Branch + OBI branch derived Bernoulli trial @@ -14284,7 +14539,7 @@ specimen can later be subject. A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. person:Chris Stoeckert - group:OBI + group:OBI kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. gene list @@ -14300,7 +14555,7 @@ specimen can later be subject. A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of particles in subset @@ -14315,7 +14570,7 @@ specimen can later be subject. A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events electronic @@ -14334,7 +14589,7 @@ specimen can later be subject. calibration substance role pH buffer used to calibrate a pH meter bears a calibration substance role - A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance + A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance Jennifer Fostel calibration substance role @@ -14377,13 +14632,13 @@ specimen can later be subject. - incubator - Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells + incubator + Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells - A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled - Frank Gibson - http://www.medterms.com/script/main/art.asp?articlekey=18426 - incubator + A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled + Frank Gibson + http://www.medterms.com/script/main/art.asp?articlekey=18426 + incubator @@ -14394,10 +14649,10 @@ specimen can later be subject. obsolete_label role - Label role is a role which inheres in a material entity and which is realized in a detection of label assay - Role Branch - label - OBI + Label role is a role which inheres in a material entity and which is realized in a detection of label assay + Role Branch + label + OBI obsolete_label role @@ -14410,12 +14665,12 @@ specimen can later be subject. - baseline participant role + baseline participant role Subject at time = 0; subject before a stress test. - a reference participant role which is realized by making the reference to qualities at the start of the study or intervention + a reference participant role which is realized by making the reference to qualities at the start of the study or intervention Person: Jennifer Fostel - baseline participant + baseline participant baseline participant role @@ -14425,11 +14680,11 @@ specimen can later be subject. - role of independent data monitoring committee + role of independent data monitoring committee a trial monitor role charged recommending whether to continue, modify, or end the trial Person: Jennifer Fostel - independent data monitoring committee + independent data monitoring committee role of independent data monitoring committee @@ -14439,11 +14694,11 @@ specimen can later be subject. - pathologist role + pathologist role a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline Person:Jennifer Fostel - Pathologist + Pathologist pathologist role @@ -14459,12 +14714,12 @@ specimen can later be subject. - supernatant collection system harvesting frame + supernatant collection system harvesting frame - A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. - Daniel Schober - google - supernatant collection system harvesting frame + A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. + Daniel Schober + google + supernatant collection system harvesting frame @@ -14479,12 +14734,12 @@ specimen can later be subject. - filter paper + filter paper - A device manufacture with the intent to provide a porous unsized paper used for filtering. - Frank Gibson - sep:00107 - filter paper + A device manufacture with the intent to provide a porous unsized paper used for filtering. + Frank Gibson + sep:00107 + filter paper @@ -14540,14 +14795,14 @@ specimen can later be subject. - role of Institutional Review Board + role of Institutional Review Board An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008 - Animal protocol review board + Animal protocol review board - the role of a organization that is realized by members reviewing study designs for their agreement with regulations - Person:Helen Parkinson + the role of a organization that is realized by members reviewing study designs for their agreement with regulations + Person:Helen Parkinson Person:Jennifer Fostel - Internal Review Board + Internal Review Board OBI, CDISC CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial. role of Institutional Review Board @@ -14563,7 +14818,7 @@ specimen can later be subject. an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures person:Jennifer Fostel - article-without-pmid-or-doi:CDISCglossary + article-without-pmid-or-doi:CDISCglossary eSource document @@ -14573,11 +14828,11 @@ specimen can later be subject. - crossover population role + crossover population role - a role realized when a participant serves as reference to itself + a role realized when a participant serves as reference to itself Person: Jennifer Fostel - crossover population + crossover population crossover population role @@ -14587,12 +14842,12 @@ specimen can later be subject. - complete nutrient role + complete nutrient role Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm - A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. + A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. Person: Jennifer Fostel - complete nutrient + complete nutrient complete nutrient role @@ -14653,7 +14908,7 @@ addition of has_role restriction An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel - CDISC glossary + CDISC glossary electronic case report form @@ -14663,12 +14918,12 @@ addition of has_role restriction - placebo role + placebo role Pill consisting of inert materials - a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance + a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance Person:Jennifer Fostel - placebo + placebo CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product. placebo role @@ -14698,7 +14953,7 @@ addition of has_role restriction A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt parameter threshold @@ -14708,12 +14963,12 @@ addition of has_role restriction - study group role - The group of randomized participants that are assigned to a treatment arm of the trial + study group role + The group of randomized participants that are assigned to a treatment arm of the trial a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol Jennifer Fostel - study group population + study group population study group role @@ -14724,14 +14979,14 @@ addition of has_role restriction p-value - PMID:19696660 + PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. - May be outside the scope of OBI long term, is needed so is retained + May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert - WEB: http://en.wikipedia.org/wiki/P-value + WEB: http://en.wikipedia.org/wiki/P-value p-value @@ -14761,7 +15016,7 @@ http://code.google.com/p/popcomm-ontology/ - + @@ -14791,15 +15046,15 @@ http://code.google.com/p/popcomm-ontology/ - - nuclear magnetic resonance 3D structure determination assay - Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). + + NMR 3D molecular structure determination assay + Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). - A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. - IEDB - PlanAndPlannedProcess Branch - IEDB - nuclear magnetic resonance 3D structure determination assay + A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. + IEDB + PlanAndPlannedProcess Branch + IEDB + NMR 3D molecular structure determination assay @@ -14816,9 +15071,9 @@ http://code.google.com/p/popcomm-ontology/ imaging assay - An assay that produces a picture of an entity. - PlanAndPlannedProcess Branch - OBI branch derived + An assay that produces a picture of an entity. + PlanAndPlannedProcess Branch + OBI branch derived imaging assay @@ -14841,11 +15096,11 @@ http://code.google.com/p/popcomm-ontology/ - role of pathology review board + role of pathology review board a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation Person: Jennifer Fostel - pathology review board + pathology review board role of pathology review board @@ -14861,14 +15116,14 @@ http://code.google.com/p/popcomm-ontology/ - microtiter plate - A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) + microtiter plate + A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) - A microtiter_plate is a flat plate with multiple wells used as small test tubes. - Melanie Courtot - microplate - http://en.wikipedia.org/wiki/Microtiter_plate - microtiter plate + A microtiter_plate is a flat plate with multiple wells used as small test tubes. + Melanie Courtot + microplate + http://en.wikipedia.org/wiki/Microtiter_plate + microtiter plate @@ -14877,15 +15132,15 @@ http://code.google.com/p/popcomm-ontology/ - role of impartial witness + role of impartial witness According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html - a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial + a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who - Person: Helen Parkinson + Person: Helen Parkinson Person: Jennifer Fostel - impartial witness + impartial witness role of impartial witness @@ -14911,12 +15166,12 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - biological replicate role + biological replicate role A member of a dose-time group; a patient in a given arm of a trial - a reference participant role realized by equivalent treatment of participants + a reference participant role realized by equivalent treatment of participants Person:Jennifer Fostel - biological replicate + biological replicate OBI biological replicate role @@ -14968,12 +15223,12 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 radioactivity detection - Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. + Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. - An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. - IEDB - PlanAndPlannedProcess Branch - IEDB + An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. + IEDB + PlanAndPlannedProcess Branch + IEDB radioactivity detection @@ -15020,19 +15275,19 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - investigation agent role + investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. - Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. + Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch - investigator + investigator OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - study person role + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) - investigation agent role + investigation agent role @@ -15047,14 +15302,14 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - nutrient role + nutrient role Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. GROUP: Role branch - nutrient + nutrient Wikipedia, feb 29, 2008 - 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. + 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. nutrient role @@ -15065,11 +15320,11 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 obsolete_dropout role - Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) + Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) - Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. - Role Branch - OBI + Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. + Role Branch + OBI obsolete_dropout role true @@ -15083,9 +15338,9 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 obsolete health care provider role - a worker role of providing medical care either within or outside the study timeline - Person:Jennifer Fostel - health care provider + a worker role of providing medical care either within or outside the study timeline + Person:Jennifer Fostel + health care provider obsolete health care provider role true @@ -15115,7 +15370,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 A digital entity intended to capture data in analytical cytology domain. person:Chris Stoeckert - group:Flow Cytometry community + group:Flow Cytometry community analytical cytology data file @@ -15125,11 +15380,11 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - proxy respondent role + proxy respondent role Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel Jennifer Fostel - proxy respondent + proxy respondent proxy respondent role @@ -15144,7 +15399,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. person:Chris Stoeckert - group:Flow Cytometry community + group:Flow Cytometry community fluorescence compensation matrix @@ -15160,12 +15415,12 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - negative reference substance role + negative reference substance role Saline solution - a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response + a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response Person: Jennifer Fostel - negative reference substance + negative reference substance negative reference substance role @@ -15175,15 +15430,15 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - role of legally acceptable representative + role of legally acceptable representative Parent of minor patient; Definition of legally acceptable representative An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE - a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. + a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary] Person: Jennifer Fostel - Person:Helen Parkinson - legally acceptable representative + Person:Helen Parkinson + legally acceptable representative OBI, CDISC role of legally acceptable representative @@ -15198,7 +15453,7 @@ An individual or juridicial or other body authorized under applicable law to con An investigation report is a report on the results of an investigation. person:Chris Stoeckert - group:OBI + group:OBI investigation results report @@ -15234,12 +15489,12 @@ An individual or juridicial or other body authorized under applicable law to con - reference subject role + reference subject role Saline treated rat; one of three identically-treated subjects a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference Jennifer Fostel - reference participant + reference participant OBI reference subject role @@ -15250,14 +15505,14 @@ An individual or juridicial or other body authorized under applicable law to con - vital dye role - typtan blue has a vital dye + vital dye role + typtan blue has a vital dye - A dye role that is realized when used to detect live cells in an experiment - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 - Person: Helen Parkinson + A dye role that is realized when used to detect live cells in an experiment + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 + Person: Helen Parkinson Person: Jennifer Fostel - vital dye + vital dye vital dye role @@ -15268,12 +15523,12 @@ An individual or juridicial or other body authorized under applicable law to con obsolete_blinded medication role - 115 patients received ipilimumab and blinded medication - Inert pill shaped like aspirin tablet + 115 patients received ipilimumab and blinded medication + Inert pill shaped like aspirin tablet - Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance - Jennifer Fostel - Person:Helen Parkinson + Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance + Jennifer Fostel + Person:Helen Parkinson obsolete_blinded medication role true @@ -15285,11 +15540,11 @@ An individual or juridicial or other body authorized under applicable law to con - sub-investigator role + sub-investigator role a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline Person: Jennifer Fostel - sub-investigator + sub-investigator CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows sub-investigator role @@ -15368,9 +15623,9 @@ An individual or juridicial or other body authorized under applicable law to con obsolete_defined_material - Place holder class, Utility class to gather the defined classes - Susanna Sansone - OBI Biomaterial derived + Place holder class, Utility class to gather the defined classes + Susanna Sansone + OBI Biomaterial derived obsolete_defined_material true @@ -15408,11 +15663,11 @@ An individual or juridicial or other body authorized under applicable law to con - trial statistician role + trial statistician role a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. Person:Jennifer Fostel - trial statistician + trial statistician CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9] trial statistician role @@ -15427,7 +15682,7 @@ An individual or juridicial or other body authorized under applicable law to con A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. person:Chris Stoeckert - group:OBI + group:OBI see P-Value standard error @@ -15444,13 +15699,13 @@ An individual or juridicial or other body authorized under applicable law to con - antigen role + antigen role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response - An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens + An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens Role Branch - OBI - 9Mar09 waiting for discussion with immunology terms + OBI + 9Mar09 waiting for discussion with immunology terms antigen role @@ -15477,7 +15732,7 @@ An individual or juridicial or other body authorized under applicable law to con a responsible party role involved with any of the following activities: initiating, managing and funding a study Person: Jennifer Fostel - sponsor + sponsor CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators sponsor role @@ -15519,11 +15774,11 @@ This leads to my proposal: We define organization through the statements 1 - current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - PERSON: Susanna Sansone - GROUP: OBI + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI organization @@ -15533,12 +15788,12 @@ for now. - feed role + feed role Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 - a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. + a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. Person: Jennifer Fostel - feed + feed OBI feed role @@ -15549,12 +15804,12 @@ for now. - technical replicate role + technical replicate role Aliquots of a tissue subjected to parallel assays - technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay + technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay Person: Jennifer Fostel - technical replicate + technical replicate technical replicate role @@ -15566,10 +15821,10 @@ for now. dye role - A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. + A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. Jennifer Fostel - dye - A substance used to color materials www.answers.com/topic/dye 19feb09 + dye + A substance used to color materials www.answers.com/topic/dye 19feb09 dye role @@ -15585,7 +15840,7 @@ for now. A data set which is a subset of data that are a similar to each other in some way. person:Allyson person:Chris Stoeckert - group:OBI + group:OBI cluster @@ -15595,14 +15850,14 @@ for now. - cohort role + cohort role In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008 a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. Jennifer Fostel - WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. - WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). - WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. + WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. + WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). + WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. cohort role @@ -15654,10 +15909,10 @@ for now. plan - The plan of researcher X to perform an experiment according to a protocol. + The plan of researcher X to perform an experiment according to a protocol. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. - This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. + This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived plan @@ -15670,13 +15925,13 @@ for now. obsolete_sample population - Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 + Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 - A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. - PERSON: Jennifer Fostel - PERSON: Philippe Rocca-Serra - recruited population - GROUP: OBI Biomaterial Branch + A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. + PERSON: Jennifer Fostel + PERSON: Philippe Rocca-Serra + recruited population + GROUP: OBI Biomaterial Branch obsolete_sample population true @@ -15706,7 +15961,7 @@ for now. A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events computer @@ -15722,7 +15977,7 @@ for now. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) - study protocol + study protocol protocol @@ -15732,12 +15987,12 @@ for now. - role of regulator of consumables and medical devices + role of regulator of consumables and medical devices FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices Person: Jennifer Fostel - drug regulatoy authority + drug regulatoy authority OBI, CDISC role of regulator of consumables and medical devices @@ -15796,13 +16051,13 @@ for now. - adding a material entity into a target - Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. + adding a material entity into a target + Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. - Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. - BP - branch derived + Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. + BP + branch derived adding a material entity into a target @@ -15825,16 +16080,16 @@ for now. - analyte role - Glucose in blood (measured in an assay to determine the concentration of glucose). + analyte role + Glucose in blood (measured in an assay to determine the concentration of glucose). A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. - interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role - pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. - qualities such as weight, color are not assayed but measured, so they do not fall into this category. - GROUP: Role Branch - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role + pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. + qualities such as weight, color are not assayed but measured, so they do not fall into this category. + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role @@ -15850,11 +16105,11 @@ for now. - disease stage + disease stage Stage II breast cancer, The timepoint of recovery from a disease a part of an occurrence of a disease process which is associated with position in the normal progression of the disease - PERSON: Bjoern peters + PERSON: Bjoern peters disease stage @@ -15909,10 +16164,10 @@ for now. - intraperitoneal injection + intraperitoneal injection - is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe - BP + is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe + BP intraperitoneal injection @@ -15932,9 +16187,9 @@ for now. Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038 a precipitate is a material entity which is output of a precipitation process - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra precipited material - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch precipitate @@ -15946,7 +16201,7 @@ for now. protein-protein interaction detection assay - An assay that determines interactions between proteins, such as protein-protein binding. + An assay that determines interactions between proteins, such as protein-protein binding. protein-protein interaction detection assay @@ -15974,13 +16229,13 @@ for now. transcription factor binding site assay - Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. + Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. - An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors - Philippe Rocca-Serra - TF binding - OBI - https://sourceforge.net/p/obi/obi-terms/767/ + An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors + Philippe Rocca-Serra + TF binding + OBI + https://sourceforge.net/p/obi/obi-terms/767/ transcription factor binding site assay @@ -15991,11 +16246,11 @@ for now. obsolete_enrollment - Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 + Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 - enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules - Bjoern Peters - IEDB + enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules + Bjoern Peters + IEDB obsolete_enrollment true @@ -16049,9 +16304,9 @@ for now. a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra eluted material - OBI Bionaterial + OBI Bionaterial eluate @@ -16061,13 +16316,13 @@ need to add mobile phase as role - material to be added role - drug added to a buffer contained in a tube; substance injected into an animal; + material to be added role + drug added to a buffer contained in a tube; substance injected into an animal; material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process - Role Branch - OBI - 9 March 09 from discussion with PA branch + Role Branch + OBI + 9 March 09 from discussion with PA branch material to be added role @@ -16079,7 +16334,7 @@ need to add mobile phase as role obsolete_peritoneum - is the serous membrane that forms the lining of the abdominal cavity + is the serous membrane that forms the lining of the abdominal cavity obsolete_peritoneum true @@ -16103,13 +16358,13 @@ need to add mobile phase as role - interpreting data - Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. + interpreting data + Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - Bjoern Peters + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + Bjoern Peters drawing a conclusion based on data @@ -16130,14 +16385,14 @@ need to add mobile phase as role - planning - The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. + planning + The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification - 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. - Bjoern Peters - Bjoern Peters - Plans and Planned Processes Branch + 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. + Bjoern Peters + Bjoern Peters + Plans and Planned Processes Branch planning @@ -16148,10 +16403,10 @@ need to add mobile phase as role obsolete_documenting - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. + Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting + Bjoern Peters + wikipedia http://en.wikipedia.org/wiki/Documenting obsolete_documenting @@ -16203,7 +16458,7 @@ need to add mobile phase as role - inductive reasoning + inductive reasoning Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. @@ -16212,8 +16467,8 @@ need to add mobile phase as role Proposal is to obsolete. - Bjoern Peters - wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning + Bjoern Peters + wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning inductive reasoning @@ -16236,14 +16491,14 @@ Proposal is to obsolete. - mass analyzer - The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation + mass analyzer + The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation - A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. - Frank Gibson - PERSON: Daniel Schober - http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer - mass analyzer + A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. + Frank Gibson + PERSON: Daniel Schober + http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer + mass analyzer @@ -16286,13 +16541,13 @@ Proposal is to obsolete. - ion source - The ion source of a Voyager-DE??? STR Biospectrometry Workstation + ion source + The ion source of a Voyager-DE??? STR Biospectrometry Workstation - An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). - Frank Gibson - http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source - ion source + An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). + Frank Gibson + http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source + ion source @@ -16307,13 +16562,13 @@ Proposal is to obsolete. - ion detector - The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation + ion detector + The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation - An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. - Frank Gibson - http://en.wikipedia.org/wiki/Mass_spectrometry#Detector - ion detector + An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. + Frank Gibson + http://en.wikipedia.org/wiki/Mass_spectrometry#Detector + ion detector @@ -16329,13 +16584,13 @@ Proposal is to obsolete. metabolite profiling assay - Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 + Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 - An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism - Philippe Rocca-Serra - metabolite assay - metabolomic assay - OBI + An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism + Philippe Rocca-Serra + metabolite assay + metabolomic assay + OBI metabolite profiling assay @@ -16348,10 +16603,10 @@ Proposal is to obsolete. light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot light emission function @@ -16364,10 +16619,10 @@ Proposal is to obsolete. record function A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot record function @@ -16380,10 +16635,10 @@ Proposal is to obsolete. magnify function A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot magnify function @@ -16394,13 +16649,13 @@ Proposal is to obsolete. contain function - A syringe, a beaker + A syringe, a beaker A contain function is a function to constrain a material entities location in space - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot contain function @@ -16413,10 +16668,10 @@ Proposal is to obsolete. heat function A heat function is a function that increases the internal kinetic energy of a material - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot heat function @@ -16429,10 +16684,10 @@ Proposal is to obsolete. material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot material separation function @@ -16460,12 +16715,12 @@ Proposal is to obsolete. - ionize process - Electrospray ionization in mass spectrometry + ionize process + Electrospray ionization in mass spectrometry - a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. - 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize - Person:Bjoern Peters + a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. + 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize + Person:Bjoern Peters ionize process @@ -16478,10 +16733,10 @@ Proposal is to obsolete. excitation function A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot excitation function @@ -16494,10 +16749,10 @@ Proposal is to obsolete. freeze function A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot freeze function @@ -16509,11 +16764,11 @@ Proposal is to obsolete. synthesizing function - A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot synthesizing function @@ -16526,10 +16781,10 @@ Proposal is to obsolete. perturb function A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot http://en.wikipedia.org/wiki/Perturbation_biology perturb function @@ -16543,7 +16798,7 @@ Proposal is to obsolete. filter function A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through - Frank Gibson + Frank Gibson filter function @@ -16556,10 +16811,10 @@ Proposal is to obsolete. mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot http://en.wikipedia.org/wiki/Mechanical_work mechanical function @@ -16573,7 +16828,7 @@ Proposal is to obsolete. gas filter function A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture - Frank Gibson + Frank Gibson gas filter function @@ -16586,7 +16841,7 @@ Proposal is to obsolete. liquid filter function A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture - Frank Gibson + Frank Gibson liquid filter function @@ -16599,10 +16854,10 @@ Proposal is to obsolete. transfer function A transfer function is a function to displace a material from one location to another. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot transfer function @@ -16613,12 +16868,12 @@ Proposal is to obsolete. electricity supply function - the function of supplying current during a neuroscience experiment. + the function of supplying current during a neuroscience experiment. An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment. - Daniel Schober - Frank Gibson - Melanie Courtot + Daniel Schober + Frank Gibson + Melanie Courtot power supply electricity supply function @@ -16630,13 +16885,13 @@ Proposal is to obsolete. ionization function - The ion source in amass spectrometer + The ion source in amass spectrometer An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot http://en.wikipedia.org/wiki/Ionization ionization function @@ -16650,9 +16905,9 @@ Proposal is to obsolete. cool function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. - Daniel Schober - Frank Gibson - Melanie Courtot + Daniel Schober + Frank Gibson + Melanie Courtot cool function @@ -16663,13 +16918,13 @@ Proposal is to obsolete. connection function - An electricity cable + An electricity cable A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot connection function @@ -16697,13 +16952,13 @@ Proposal is to obsolete. - isoelectric focusing device + isoelectric focusing device - An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. - Frank Gibson - isoelectric focusing unit - sep:00097 - isoelectric focusing device + An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. + Frank Gibson + isoelectric focusing unit + sep:00097 + isoelectric focusing device @@ -16724,12 +16979,12 @@ Proposal is to obsolete. - thermostatic circulator + thermostatic circulator - A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid - Frank Gibson - sep:00098 - thermostatic circulator + A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid + Frank Gibson + sep:00098 + thermostatic circulator @@ -16741,7 +16996,7 @@ Proposal is to obsolete. energy supply function An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy - Frank Gibson + Frank Gibson energy supply function @@ -16766,7 +17021,7 @@ Proposal is to obsolete. information processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. - Frank Gibson + Frank Gibson data processor function information processor function @@ -16780,11 +17035,11 @@ Proposal is to obsolete. signal conversion function A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - transduction function + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + transduction function signal conversion function @@ -16800,12 +17055,12 @@ Proposal is to obsolete. - blot module + blot module - A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised - Frank Gibson - sep:00092 - blot module + A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised + Frank Gibson + sep:00092 + blot module @@ -16817,10 +17072,10 @@ Proposal is to obsolete. signal amplification function A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot signal amplification function @@ -16845,7 +17100,7 @@ Proposal is to obsolete. image acquisition function An image acquisition function is a function to acquire an image of a material - Frank Gibson + Frank Gibson image acquisition function @@ -16866,13 +17121,13 @@ Proposal is to obsolete. - image acquisition device + image acquisition device - An image creation device is a device which captures a digitized image of an object - Frank Gibson - image acquisition device - sep:00096 - image creation device + An image creation device is a device which captures a digitized image of an object + Frank Gibson + image acquisition device + sep:00096 + image creation device @@ -16881,13 +17136,13 @@ Proposal is to obsolete. - solid support function - Taped, glued, pinned, dried or molecularly bonded to a solid support + solid support function + Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement - Daniel Schober - Frank Gibson - Melanie Courtot + Daniel Schober + Frank Gibson + Melanie Courtot solid support function @@ -16900,10 +17155,10 @@ Proposal is to obsolete. display function A display function is a function to present information by translating that information through some lookup process into visual form. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot display function @@ -16916,10 +17171,10 @@ Proposal is to obsolete. environment control function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot environment control function @@ -16932,9 +17187,9 @@ Proposal is to obsolete. sort function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. - Daniel Schober - Frank Gibson - Melanie Courtot + Daniel Schober + Frank Gibson + Melanie Courtot sort function @@ -16956,12 +17211,12 @@ Proposal is to obsolete. - gel dryer + gel dryer - A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels - Frank Gibson - sep:00094 - gel dryer + A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels + Frank Gibson + sep:00094 + gel dryer @@ -16976,10 +17231,10 @@ Proposal is to obsolete. - primer role + primer role - a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. - (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer + a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. + (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer primer role @@ -17002,12 +17257,12 @@ Proposal is to obsolete. PCR product - PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. + PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. is double stranded DNA that is the specified output of a polymerase chain reaction We are using PCR and not the written out words, as this is the most common used. - GROUP: OBI BIomaterial Branch - GROUP: OBI BIomaterial Branch + GROUP: OBI BIomaterial Branch + GROUP: OBI BIomaterial Branch PCR product @@ -17023,11 +17278,11 @@ Proposal is to obsolete. - viral RNA extraction - The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 + viral RNA extraction + The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 - The extraction of RNA from an input material that specifically isolates viral RNA - Person:Bjoern Peters + The extraction of RNA from an input material that specifically isolates viral RNA + Person:Bjoern Peters viral RNA extraction @@ -17049,10 +17304,10 @@ Proposal is to obsolete. - nucleic acid template role - a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 + nucleic acid template role + a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 - a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. + a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. nucleic acid template role @@ -17076,11 +17331,11 @@ Proposal is to obsolete. recombinant plasmid - a plasmid in which extraneous DNA has been inserted. - PERSON: Bjoern Peters - PERSON: Kevin Clancy - PERSON: Melanie Courtot - GROUP: OBI Biomaterial Branch + a plasmid in which extraneous DNA has been inserted. + PERSON: Bjoern Peters + PERSON: Kevin Clancy + PERSON: Melanie Courtot + GROUP: OBI Biomaterial Branch recombinant plasmid @@ -17104,12 +17359,12 @@ Proposal is to obsolete. - cloning vector role - pBluescript plays the role of a cloning vector + cloning vector role + pBluescript plays the role of a cloning vector A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/ - PERSON: Helen Parkinson + PERSON: Helen Parkinson cloning vector role @@ -17137,12 +17392,12 @@ Proposal is to obsolete. - cell cycle synchronization + cell cycle synchronization Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs. a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle - OBI PA - Bjoern Peters and Nicole Washington + OBI PA + Bjoern Peters and Nicole Washington cell cycle synchronization @@ -17186,13 +17441,13 @@ Proposal is to obsolete. - polymerase chain reaction + polymerase chain reaction Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. - OBI Plan + OBI Plan PCR - adapted from wikipedai + adapted from wikipedai polymerase chain reaction @@ -17202,12 +17457,12 @@ Proposal is to obsolete. - cloning insert role + cloning insert role cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. - Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" - GROUP: Role branch - OBII and Wikipedia + Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" + GROUP: Role branch + OBII and Wikipedia cloning insert role @@ -17276,11 +17531,11 @@ Proposal is to obsolete. measuring glucose concentration in blood serum assay - Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319. + Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319. - An assay that determines the concentration of glucose molecules in a blood serum sample - Bjoern Peters - OBI + An assay that determines the concentration of glucose molecules in a blood serum sample + Bjoern Peters + OBI measuring glucose concentration in blood serum assay @@ -17310,8 +17565,8 @@ Proposal is to obsolete. enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) - person:Melanie Courtot - group:OBI + person:Melanie Courtot + group:OBI reverse transcriptase @@ -17322,10 +17577,10 @@ activity) obsolete_trypsinized material - A trypsinized suspension of cells + A trypsinized suspension of cells - A material entity that has undergone a process of digestion with trypsin - Person:Bjoern Peters + A material entity that has undergone a process of digestion with trypsin + Person:Bjoern Peters obsolete_trypsinized material true @@ -17343,13 +17598,13 @@ activity) - syringe - Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 + syringe + Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 - A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw - Philippe Rocca-Serra - OBI Instrument adapted from Wikipedia - syringe + A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw + Philippe Rocca-Serra + OBI Instrument adapted from Wikipedia + syringe @@ -17368,9 +17623,9 @@ activity) Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra extracted material - GROUP: OBI Biomatrial Branch + GROUP: OBI Biomatrial Branch extract @@ -17473,14 +17728,14 @@ activity) transcription profiling assay - Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 - - An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. - This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. - Philippe Rocca-Serra - gene expression profiling - transcription profiling - OBI + Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 + + An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. + This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. + Philippe Rocca-Serra + gene expression profiling + transcription profiling + OBI transcription profiling assay @@ -17494,9 +17749,9 @@ activity) A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi averaging objective @@ -17536,12 +17791,12 @@ activity) - injection + injection Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. - Philippe Rocca-Serra - OBI Biomaterial + Philippe Rocca-Serra + OBI Biomaterial injection @@ -17590,10 +17845,10 @@ activity) (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) - MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything + MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. - person: Melanie Courtot - GROUP:OBI + person: Melanie Courtot + GROUP:OBI enzyme @@ -17633,11 +17888,11 @@ that has_part some material entity is a material entity. If we add as equivalent - intraperitoneal administration - Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h + intraperitoneal administration + Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h - The administration of a substance into the peritoneum of an organism - Person:Bjoern Peters + The administration of a substance into the peritoneum of an organism + Person:Bjoern Peters intraperitoneal administration @@ -17671,8 +17926,8 @@ that has_part some material entity is a material entity. If we add as equivalent plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 - person:Melanie Courtot - group:OBI + person:Melanie Courtot + group:OBI plasmid @@ -17726,11 +17981,11 @@ that has_part some material entity is a material entity. If we add as equivalent - injection into organ section - Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology + injection into organ section + Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology - A process in which an input substance is injected into a organ section. - Person:Bjoern Peters + A process in which an input substance is injected into a organ section. + Person:Bjoern Peters injection into organ section @@ -17756,9 +18011,9 @@ that has_part some material entity is a material entity. If we add as equivalent Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143 a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution - PERSON: Jie Zheng - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch + PERSON: Jie Zheng + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch polyacrylamide gel @@ -17809,12 +18064,12 @@ that has_part some material entity is a material entity. If we add as equivalent DNA sequence feature detection assay - genotyping using an Affymetrix chip + genotyping using an Affymetrix chip - An assay with the objective to determine a sequence feature of DNA - Bjoern Peters - Philippe Rocca-Serra - OBI + An assay with the objective to determine a sequence feature of DNA + Bjoern Peters + Philippe Rocca-Serra + OBI DNA sequence feature detection assay @@ -17824,11 +18079,11 @@ that has_part some material entity is a material entity. If we add as equivalent - adding material objective - creating a mouse infected with LCM virus + adding material objective + creating a mouse infected with LCM virus is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity - BP + BP adding material objective @@ -17901,13 +18156,13 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 + High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. - Philippe Rocca-Serra - SNP analysis - genotype profiling - OBI Biomaterial + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + Philippe Rocca-Serra + SNP analysis + genotype profiling + OBI Biomaterial genotyping assay @@ -17923,13 +18178,13 @@ that has_part some material entity is a material entity. If we add as equivalent - needle - Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 + needle + Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 - A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. - Philippe Rocca-Serra - OBI Instrument - needle + A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. + Philippe Rocca-Serra + OBI Instrument + needle @@ -17938,12 +18193,12 @@ that has_part some material entity is a material entity. If we add as equivalent - analyte measurement objective - The objective to measure the concentration of glucose in a blood sample + analyte measurement objective + The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant - PERSON: Bjoern Peters - PPPB branch + PERSON: Bjoern Peters + PPPB branch analyte measurement objective @@ -17972,11 +18227,11 @@ that has_part some material entity is a material entity. If we add as equivalent DNA sequence variation detection assay - Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 + Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 - An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. - Philippe Rocca-Serra - OBI Biomaterial + An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. + Philippe Rocca-Serra + OBI Biomaterial DNA sequence variation detection assay @@ -17996,8 +18251,8 @@ that has_part some material entity is a material entity. If we add as equivalent Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269 a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch agarose gel @@ -18007,12 +18262,12 @@ that has_part some material entity is a material entity. If we add as equivalent - assay objective - the objective to determine the weight of a mouse. + assay objective + the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) - PPPB branch - PPPB branch + PPPB branch + PPPB branch assay objective @@ -18023,11 +18278,11 @@ that has_part some material entity is a material entity. If we add as equivalent obsolete_heart - Alan Ruttenberg's heart + Alan Ruttenberg's heart - The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions - Person:Bjoern Peters - http://en.wikipedia.org/wiki/Heart + The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions + Person:Bjoern Peters + http://en.wikipedia.org/wiki/Heart obsolete_heart true @@ -18052,18 +18307,18 @@ that has_part some material entity is a material entity. If we add as equivalent analyte assay - example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output - - An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. - Alan Ruttenberg - Bjoern Peters - Helen Parkinson - Philippe Rocca-Serra - Alan Ruttenberg - Bjoern Peters - Helen Parkinson - OBI Planned process branch - Philippe Rocca-Serra + example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output + + An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. + Alan Ruttenberg + Bjoern Peters + Helen Parkinson + Philippe Rocca-Serra + Alan Ruttenberg + Bjoern Peters + Helen Parkinson + OBI Planned process branch + Philippe Rocca-Serra analyte assay @@ -18085,13 +18340,13 @@ that has_part some material entity is a material entity. If we add as equivalent - target of material addition role - peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. + target of material addition role + peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. - target of material addition role is a role realized by an entity into which a material is added in a material addition process - From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. - GROUP: Role Branch - OBI + target of material addition role is a role realized by an entity into which a material is added in a material addition process + From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. + GROUP: Role Branch + OBI target of material addition role @@ -18142,11 +18397,11 @@ that has_part some material entity is a material entity. If we add as equivalent mass measurement assay - The patients was weighed and mass was determined to be 47 kilograms + The patients was weighed and mass was determined to be 47 kilograms - An assay that determines the mass of an evaluant - Helen Parkinson - OBI + An assay that determines the mass of an evaluant + Helen Parkinson + OBI mass measurement assay @@ -18157,10 +18412,10 @@ that has_part some material entity is a material entity. If we add as equivalent obsolete_identification - DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 + DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 - a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval - Philippe Rocca-Serra + a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval + Philippe Rocca-Serra obsolete_identification true @@ -18191,9 +18446,9 @@ that has_part some material entity is a material entity. If we add as equivalent intra cellular electrophysiology recording assay - An electrophysiology recording assay where the recording location of the electrode is intracellular - Frank Gibson - Frank Gibson + An electrophysiology recording assay where the recording location of the electrode is intracellular + Frank Gibson + Frank Gibson intra cellular electrophysiology recording assay @@ -18203,13 +18458,13 @@ that has_part some material entity is a material entity. If we add as equivalent - packed column + packed column - A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. - PERSON:Daniel Schober - WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 - packed column + A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. + PERSON:Daniel Schober + WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 + packed column @@ -18219,12 +18474,12 @@ that has_part some material entity is a material entity. If we add as equivalent obsolete_defined_output - example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. + example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. - This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. - PERSON: Alan Ruttenberg - PERSON: James Malone - PERSON: Melanie Courtot + This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. + PERSON: Alan Ruttenberg + PERSON: James Malone + PERSON: Melanie Courtot obsolete_defined_output true @@ -18248,11 +18503,11 @@ that has_part some material entity is a material entity. If we add as equivalent regulatory agency - The US Environmental Protection Agency + The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. - GROUP: OBI Biomaterial Branch - WEB: en.wikipedia.org/wiki/Regulator + GROUP: OBI Biomaterial Branch + WEB: en.wikipedia.org/wiki/Regulator regulatory agency @@ -18268,11 +18523,11 @@ that has_part some material entity is a material entity. If we add as equivalent - normalized data set + normalized data set A data set that is produced as the output of a normalization data transformation. - PERSON: James Malone - PERSON: Melanie Courtot + PERSON: James Malone + PERSON: Melanie Courtot normalized data set @@ -18300,13 +18555,13 @@ that has_part some material entity is a material entity. If we add as equivalent measure function - A glucometer measures blood glucose concentration, the glucometer has a measure function. + A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. - PERSON: Daniel Schober - PERSON: Helen Parkinson - PERSON: Melanie Courtot - PERSON:Frank Gibson + PERSON: Daniel Schober + PERSON: Helen Parkinson + PERSON: Melanie Courtot + PERSON:Frank Gibson measure function @@ -18334,12 +18589,12 @@ that has_part some material entity is a material entity. If we add as equivalent extracellular electrophysiology recording assay - The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron + The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron - An electrophysiology recording assay where the recording location of the electrode is extracellular - Frank Gibson - Helen Parkinson - Frank Gibson + An electrophysiology recording assay where the recording location of the electrode is extracellular + Frank Gibson + Helen Parkinson + Frank Gibson extracellular electrophysiology recording assay @@ -18358,9 +18613,9 @@ that has_part some material entity is a material entity. If we add as equivalent consume data function Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. - PERSON: Daniel Schober - PERSON: Frank Gibson - PERSON: Melanie Courtot + PERSON: Daniel Schober + PERSON: Frank Gibson + PERSON: Melanie Courtot consume data function @@ -18370,17 +18625,17 @@ that has_part some material entity is a material entity. If we add as equivalent - material transformation objective - The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra artifact creation objective - GROUP: OBI PlanAndPlannedProcess Branch + GROUP: OBI PlanAndPlannedProcess Branch material transformation objective @@ -18408,17 +18663,17 @@ that has_part some material entity is a material entity. If we add as equivalent - manufacturing + manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process - Manufacturing implies reproducibility and responsibility AR + Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - GROUP: OBI PlanAndPlannedProcess Branch + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch manufacturing @@ -18428,15 +18683,15 @@ that has_part some material entity is a material entity. If we add as equivalent - manufacturing objective + manufacturing objective is the objective to manufacture a material of a certain function (device) - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - GROUP: OBI PlanAndPlannedProcess Branch + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective @@ -18452,14 +18707,14 @@ that has_part some material entity is a material entity. If we add as equivalent - column chromatography detector + column chromatography detector - There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 - chromatography detector, defined class/xps - column chromatography detector + There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 + chromatography detector, defined class/xps + column chromatography detector @@ -18468,13 +18723,13 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker autosampler + Bruker autosampler - A Bruker autosampler is an autosampler made by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 - Bruker autosampler + A Bruker autosampler is an autosampler made by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 + Bruker autosampler @@ -18483,13 +18738,13 @@ that has_part some material entity is a material entity. If we add as equivalent - organic acid column + organic acid column - An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 - organic acid column + An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 + organic acid column @@ -18498,14 +18753,14 @@ that has_part some material entity is a material entity. If we add as equivalent - thermal conductivity detector + thermal conductivity detector - The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). - PERSON:Daniel Schober - TCD, hot wire detector - WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 - thermal conductivity detector + The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). + PERSON:Daniel Schober + TCD, hot wire detector + WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 + thermal conductivity detector @@ -18514,14 +18769,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker US 2 NMR magnet + Bruker US 2 NMR magnet - An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 - NMR instrument - Bruker US 2 NMR magnet + An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 + NMR instrument + Bruker US 2 NMR magnet @@ -18530,14 +18785,14 @@ that has_part some material entity is a material entity. If we add as equivalent - protein column + protein column - A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 - refactor as defined class - protein column + A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 + refactor as defined class + protein column @@ -18546,14 +18801,14 @@ that has_part some material entity is a material entity. If we add as equivalent - solvent mixer + solvent mixer - A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 - check on definition ! - solvent mixer + A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 + check on definition ! + solvent mixer @@ -18561,37 +18816,42 @@ that has_part some material entity is a material entity. If we add as equivalent - - + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - + + mass spectrometry assay - Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. + Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. - An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. - Philippe Rocca-Serra - Philippe Rocca-Serra + An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. + Philippe Rocca-Serra + Philippe Rocca-Serra mass spectrometry assay @@ -18617,15 +18877,15 @@ that has_part some material entity is a material entity. If we add as equivalent - study design execution - injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. + study design execution + injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. - a planned process that carries out a study design - removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. - branch derived - 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. + a planned process that carries out a study design + removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. + branch derived + 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution + study design execution @@ -18634,14 +18894,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker NMR Case sample changer + Bruker NMR Case sample changer - The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 - NMR instrument - Bruker NMR Case sample changer + The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 + NMR instrument + Bruker NMR Case sample changer @@ -18650,13 +18910,13 @@ that has_part some material entity is a material entity. If we add as equivalent - nano pump system + nano pump system - A pump system optimized for nano flow chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 - nano pump system + A pump system optimized for nano flow chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 + nano pump system @@ -18665,14 +18925,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker AutoClean system + Bruker AutoClean system - NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. - washing system/NMR tube washing system, XPS: device has function washing - PERSON:Daniel Schober - WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 - Bruker AutoClean system + NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. + washing system/NMR tube washing system, XPS: device has function washing + PERSON:Daniel Schober + WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 + Bruker AutoClean system @@ -18681,13 +18941,13 @@ that has_part some material entity is a material entity. If we add as equivalent - manual injection system + manual injection system - The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 - manual injection system + The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 + manual injection system @@ -18696,14 +18956,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Varian GEMINI spectrometer + Varian GEMINI spectrometer - An older Varian Broadband NMR spectrometer. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 - NMR instrument - Varian GEMINI spectrometer + An older Varian Broadband NMR spectrometer. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 + NMR instrument + Varian GEMINI spectrometer @@ -18712,14 +18972,14 @@ that has_part some material entity is a material entity. If we add as equivalent - column connector + column connector - A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 - chromatography device - column connector + A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 + chromatography device + column connector @@ -18728,14 +18988,14 @@ that has_part some material entity is a material entity. If we add as equivalent - solid NMR probe + solid NMR probe - An NMR probe that is designed to hold a solid sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 - NMR device - solid NMR probe + An NMR probe that is designed to hold a solid sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 + NMR device + solid NMR probe @@ -18744,15 +19004,15 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker high resolution probe + Bruker high resolution probe - BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. - PERSON:Daniel Schober - HR Probe - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 - NMR probe - Bruker high resolution probe + BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. + PERSON:Daniel Schober + HR Probe + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 + NMR probe + Bruker high resolution probe @@ -18761,13 +19021,13 @@ that has_part some material entity is a material entity. If we add as equivalent - chromatography detector + chromatography detector - A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 - chromatography detector + A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 + chromatography detector @@ -18776,13 +19036,13 @@ that has_part some material entity is a material entity. If we add as equivalent - normal phase column + normal phase column - A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 - normal phase column + A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 + normal phase column @@ -18791,14 +19051,14 @@ that has_part some material entity is a material entity. If we add as equivalent - APOLLO console + APOLLO console - The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. - PERSON:Daniel Schober - WEB:<http://www.tecmag.com/apollo.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 - NMR instrument/NMR console - APOLLO console + The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. + PERSON:Daniel Schober + WEB:<http://www.tecmag.com/apollo.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 + NMR instrument/NMR console + APOLLO console @@ -18807,14 +19067,14 @@ that has_part some material entity is a material entity. If we add as equivalent - NMR sample holder + NMR sample holder - An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 - NMR device - NMR sample holder + An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 + NMR device + NMR sample holder @@ -18829,14 +19089,14 @@ that has_part some material entity is a material entity. If we add as equivalent - chromatography instrument + chromatography instrument - Any instrument that is used to carry out a chromatography experiment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 - chromatography device, defined class? - chromatography instrument + Any instrument that is used to carry out a chromatography experiment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 + chromatography device, defined class? + chromatography instrument @@ -18845,14 +19105,14 @@ that has_part some material entity is a material entity. If we add as equivalent - continuous wave NMR instrument + continuous wave NMR instrument - Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). - PERSON:Daniel Schober - WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 - NMR instrument - continuous wave NMR instrument + Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). + PERSON:Daniel Schober + WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 + NMR instrument + continuous wave NMR instrument @@ -18861,14 +19121,14 @@ that has_part some material entity is a material entity. If we add as equivalent - fourier transformation NMR instrument + fourier transformation NMR instrument - In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. - PERSON:Daniel Schober - GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 - NMR instrument - fourier transformation NMR instrument + In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. + PERSON:Daniel Schober + GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 + NMR instrument + fourier transformation NMR instrument @@ -18877,13 +19137,13 @@ that has_part some material entity is a material entity. If we add as equivalent - nitrogen phosphorous detector + nitrogen phosphorous detector - The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 - nitrogen phosphorous detector + The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 + nitrogen phosphorous detector @@ -18892,13 +19152,13 @@ that has_part some material entity is a material entity. If we add as equivalent - cation exchange column + cation exchange column - A cation exchange column is a chromatography column that is used in cation exchange chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 - cation exchange column + A cation exchange column is a chromatography column that is used in cation exchange chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 + cation exchange column @@ -18907,14 +19167,14 @@ that has_part some material entity is a material entity. If we add as equivalent - direct detection NMR probe + direct detection NMR probe - An NMR probe designed to allow the direct detection of acquisition nuclei. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 - NMR device - direct detection NMR probe + An NMR probe designed to allow the direct detection of acquisition nuclei. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 + NMR device + direct detection NMR probe @@ -18923,14 +19183,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker B-ACS system + Bruker B-ACS system - The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 - NMR instrument - Bruker B-ACS system + The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 + NMR instrument + Bruker B-ACS system @@ -18945,13 +19205,13 @@ that has_part some material entity is a material entity. If we add as equivalent - rapid resolution column + rapid resolution column - A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 - rapid resolution column + A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 + rapid resolution column @@ -18960,13 +19220,13 @@ that has_part some material entity is a material entity. If we add as equivalent - liquid chromatography autosampler + liquid chromatography autosampler - Designed to perform capillary LC with injection of sample volumes ranging from nL to L. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 - liquid chromatography autosampler + Designed to perform capillary LC with injection of sample volumes ranging from nL to L. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 + liquid chromatography autosampler @@ -18975,13 +19235,13 @@ that has_part some material entity is a material entity. If we add as equivalent - vacuum degasser + vacuum degasser - A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/vacuum.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 - vacuum degasser + A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/vacuum.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 + vacuum degasser @@ -18990,13 +19250,13 @@ that has_part some material entity is a material entity. If we add as equivalent - capillary column + capillary column - A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 - capillary column + A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 + capillary column @@ -19005,14 +19265,14 @@ that has_part some material entity is a material entity. If we add as equivalent - sample inlet + sample inlet - The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. - PERSON:Daniel Schober - WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 - chromatography device - sample inlet + The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. + PERSON:Daniel Schober + WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 + chromatography device + sample inlet @@ -19021,14 +19281,14 @@ that has_part some material entity is a material entity. If we add as equivalent - NMR tube washing system + NMR tube washing system - An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 - NMR instrument - NMR tube washing system + An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 + NMR instrument + NMR tube washing system @@ -19037,14 +19297,14 @@ that has_part some material entity is a material entity. If we add as equivalent - NMR console + NMR console - A component of an NMR instrument that controls the activities of the other components. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 - NMR instrument, TODO: same as or part of acquisition computer? - NMR console + A component of an NMR instrument that controls the activities of the other components. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 + NMR instrument, TODO: same as or part of acquisition computer? + NMR console @@ -19053,13 +19313,13 @@ that has_part some material entity is a material entity. If we add as equivalent - dual loop autosampler + dual loop autosampler - A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). - PERSON:Daniel Schober - WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 - dual loop autosampler + A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). + PERSON:Daniel Schober + WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 + dual loop autosampler @@ -19074,13 +19334,13 @@ that has_part some material entity is a material entity. If we add as equivalent - variable wavelength detector + variable wavelength detector - A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 - variable wavelength detector + A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 + variable wavelength detector @@ -19089,15 +19349,15 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker LC-NMR platform + Bruker LC-NMR platform - The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 - NMR instrument - hyphenated NMR instrument platform - Bruker LC-NMR platform + The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 + NMR instrument + hyphenated NMR instrument platform + Bruker LC-NMR platform @@ -19106,14 +19366,14 @@ that has_part some material entity is a material entity. If we add as equivalent - sample injection system + sample injection system - An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 - chromatography device - sample injection system + An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 + chromatography device + sample injection system @@ -19128,13 +19388,13 @@ that has_part some material entity is a material entity. If we add as equivalent - multiple wavelength detector + multiple wavelength detector - A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 - multiple wavelength detector + A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 + multiple wavelength detector @@ -19143,14 +19403,14 @@ that has_part some material entity is a material entity. If we add as equivalent - photoionization detector + photoionization detector - The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. - PERSON:Daniel Schober - PID - WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 - photoionization detector + The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. + PERSON:Daniel Schober + PID + WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 + photoionization detector @@ -19159,14 +19419,14 @@ that has_part some material entity is a material entity. If we add as equivalent - gas generator + gas generator - An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 - gas chromatography equipment - gas generator + An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 + gas chromatography equipment + gas generator @@ -19175,14 +19435,14 @@ that has_part some material entity is a material entity. If we add as equivalent - column jacket + column jacket - A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 - chromatography device - column jacket + A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 + chromatography device + column jacket @@ -19191,14 +19451,14 @@ that has_part some material entity is a material entity. If we add as equivalent - electron capture detector + electron capture detector - The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. - PERSON:Daniel Schober - ECD - WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 - electron capture detector + The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. + PERSON:Daniel Schober + ECD + WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 + electron capture detector @@ -19207,13 +19467,13 @@ that has_part some material entity is a material entity. If we add as equivalent - reversed phase column + reversed phase column - A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 - reversed phase column + A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 + reversed phase column @@ -19222,13 +19482,13 @@ that has_part some material entity is a material entity. If we add as equivalent - injector lubricant + injector lubricant - A lubricant used in liquid chromatography that eases sample injector penetration. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 - injector lubricant + A lubricant used in liquid chromatography that eases sample injector penetration. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 + injector lubricant @@ -19255,12 +19515,12 @@ that has_part some material entity is a material entity. If we add as equivalent - isolation of cell population - removing CD4+ cells from PBMCs using magnetic beads. + isolation of cell population + removing CD4+ cells from PBMCs using magnetic beads. - a process in which a population of cells with certain characteristics is isolated from a larger population - Person: Bjoern Peters - isolation of cell population + a process in which a population of cells with certain characteristics is isolated from a larger population + Person: Bjoern Peters + isolation of cell population @@ -19269,14 +19529,14 @@ that has_part some material entity is a material entity. If we add as equivalent - DISCOVERY console + DISCOVERY console - The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 - NMR instrument/NMR console - DISCOVERY console + The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 + NMR instrument/NMR console + DISCOVERY console @@ -19285,14 +19545,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker AMX series NMR instrument + Bruker AMX series NMR instrument - A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. - PERSON:Daniel Schober - WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 - NMR instrument - Bruker AMX series NMR instrument + A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. + PERSON:Daniel Schober + WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 + NMR instrument + Bruker AMX series NMR instrument @@ -19301,13 +19561,13 @@ that has_part some material entity is a material entity. If we add as equivalent - chromatofocusing column + chromatofocusing column - A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. - PERSON:Daniel Schober - WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 - chromatofocusing column + A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. + PERSON:Daniel Schober + WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 + chromatofocusing column @@ -19328,14 +19588,14 @@ that has_part some material entity is a material entity. If we add as equivalent - NMR probe + NMR probe - Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 - NMR instrument - NMR probe + Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 + NMR instrument + NMR probe @@ -19344,14 +19604,14 @@ that has_part some material entity is a material entity. If we add as equivalent - NMR magnet + NMR magnet - A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 - NMR instrument - NMR magnet + A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 + NMR instrument + NMR magnet @@ -19360,13 +19620,13 @@ that has_part some material entity is a material entity. If we add as equivalent - trap column + trap column - A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 - trap column + A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 + trap column @@ -19375,14 +19635,14 @@ that has_part some material entity is a material entity. If we add as equivalent - flow probe + flow probe - An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. - PERSON:Daniel Schober - WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 - NMR device - flow probe + An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. + PERSON:Daniel Schober + WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 + NMR device + flow probe @@ -19450,13 +19710,13 @@ that has_part some material entity is a material entity. If we add as equivalent clinical chemistry assay - Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. + Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. - Philippe Rocca-Serra - chemical pathology - detection of analyte in blood sample - url:https://en.wikipedia.org/wiki/Clinical_chemistry + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. + Philippe Rocca-Serra + chemical pathology + detection of analyte in blood sample + url:https://en.wikipedia.org/wiki/Clinical_chemistry clinical chemistry assay @@ -19466,14 +19726,14 @@ that has_part some material entity is a material entity. If we add as equivalent - flame ionization detector + flame ionization detector - A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. - PERSON:Daniel Schober - FID - WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 - flame ionization detector + A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. + PERSON:Daniel Schober + FID + WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 + flame ionization detector @@ -19481,14 +19741,13 @@ that has_part some material entity is a material entity. If we add as equivalent - - vial + + vial - A vial is a cylindrical container often made from glass tubing. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 - vial + A container made from solid material and primarily used for holding liquid. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Vial + vial @@ -19503,15 +19762,15 @@ that has_part some material entity is a material entity. If we add as equivalent - magic angle spinning rotor + magic angle spinning rotor - A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. - PERSON:Daniel Schober - MAS rotor - WEB:<http://www.freepatentsonline.com/4352066.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 - NMR instrument - magic angle spinning rotor + A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. + PERSON:Daniel Schober + MAS rotor + WEB:<http://www.freepatentsonline.com/4352066.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 + NMR instrument + magic angle spinning rotor @@ -19520,14 +19779,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Varian VXR spectrometer + Varian VXR spectrometer - A Varian NMR spectrometer. - PERSON:Daniel Schober - WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 - NMR instrument - Varian VXR spectrometer + A Varian NMR spectrometer. + PERSON:Daniel Schober + WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 + NMR instrument + Varian VXR spectrometer @@ -19536,13 +19795,13 @@ that has_part some material entity is a material entity. If we add as equivalent - splitless GC injector + splitless GC injector - Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. - PERSON:Daniel Schober - WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 - splitless GC injector + Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. + PERSON:Daniel Schober + WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 + splitless GC injector @@ -19551,13 +19810,13 @@ that has_part some material entity is a material entity. If we add as equivalent - preparative autosampler + preparative autosampler - For preparative LC with injection of sample volumes ranging from L to mL ranges. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 - preparative autosampler + For preparative LC with injection of sample volumes ranging from L to mL ranges. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 + preparative autosampler @@ -19566,15 +19825,15 @@ that has_part some material entity is a material entity. If we add as equivalent - flow high resolution probe + flow high resolution probe - Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. - PERSON:Daniel Schober - flow HR-probe - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 - NMR probe - flow high resolution probe + Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. + PERSON:Daniel Schober + flow HR-probe + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 + NMR probe + flow high resolution probe @@ -19583,14 +19842,14 @@ that has_part some material entity is a material entity. If we add as equivalent - liquid chromatography valve + liquid chromatography valve - A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 - chromatography device - liquid chromatography valve + A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 + chromatography device + liquid chromatography valve @@ -19599,14 +19858,14 @@ that has_part some material entity is a material entity. If we add as equivalent - JEOL NMR probe + JEOL NMR probe - An NMR probe that is manufactured by JEOL. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 - NMR device - JEOL NMR probe + An NMR probe that is manufactured by JEOL. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 + NMR device + JEOL NMR probe @@ -19615,14 +19874,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker UltraShield Plus NMR magnet + Bruker UltraShield Plus NMR magnet - An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 - NMR instrument - Bruker UltraShield Plus NMR magnet + An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 + NMR instrument + Bruker UltraShield Plus NMR magnet @@ -19631,14 +19890,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker CryoProbe + Bruker CryoProbe - The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 - NMR probe - Bruker CryoProbe + The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 + NMR probe + Bruker CryoProbe @@ -19647,14 +19906,14 @@ that has_part some material entity is a material entity. If we add as equivalent - column cartridge + column cartridge - A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 - chromatography device, check on definition ! - column cartridge + A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 + chromatography device, check on definition ! + column cartridge @@ -19663,13 +19922,13 @@ that has_part some material entity is a material entity. If we add as equivalent - affinity column + affinity column - An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 - affinity column + An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 + affinity column @@ -19678,14 +19937,14 @@ that has_part some material entity is a material entity. If we add as equivalent - tecmag NMR instrument + tecmag NMR instrument - An NMR instrument that is manufactured by tecmag. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 - NMR instrument - tecmag NMR instrument + An NMR instrument that is manufactured by tecmag. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 + NMR instrument + tecmag NMR instrument @@ -19694,13 +19953,13 @@ that has_part some material entity is a material entity. If we add as equivalent - gel filtration column + gel filtration column - A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 - gel filtration column + A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 + gel filtration column @@ -19709,13 +19968,13 @@ that has_part some material entity is a material entity. If we add as equivalent - fraction collector + fraction collector - A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 - fraction collector + A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 + fraction collector @@ -19742,11 +20001,11 @@ that has_part some material entity is a material entity. If we add as equivalent copy number variation profiling assay - Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 + Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 - An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping - Philippe Rocca-Serra - CNV analysis + An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping + Philippe Rocca-Serra + CNV analysis copy number variation profiling assay @@ -19756,13 +20015,13 @@ that has_part some material entity is a material entity. If we add as equivalent - in-line filter + in-line filter - A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. - PERSON:Daniel Schober - WEB:<http://www.appliedporous.com/frits-chromatography.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 - in-line filter + A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. + PERSON:Daniel Schober + WEB:<http://www.appliedporous.com/frits-chromatography.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 + in-line filter @@ -19771,14 +20030,14 @@ that has_part some material entity is a material entity. If we add as equivalent - imaging NMR probe + imaging NMR probe - An NMR probe that is designed for generating pictures from sample states via NMR imaging. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 - NMR device - imaging NMR probe + An NMR probe that is designed for generating pictures from sample states via NMR imaging. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 + NMR device + imaging NMR probe @@ -19799,10 +20058,10 @@ that has_part some material entity is a material entity. If we add as equivalent - isolation of adherent cells + isolation of adherent cells - a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. - isolation of adherent cells + a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. + isolation of adherent cells @@ -19811,14 +20070,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker AC series NMR instrument + Bruker AC series NMR instrument - A series of older Bruker NMR magnets, now out of production. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 - NMR instrument - Bruker AC series NMR instrument + A series of older Bruker NMR magnets, now out of production. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 + NMR instrument + Bruker AC series NMR instrument @@ -19827,14 +20086,14 @@ that has_part some material entity is a material entity. If we add as equivalent - gas chromatography equipment + gas chromatography equipment - Any device used in a gas chromatography experiment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 - will become defined class/xps - gas chromatography equipment + Any device used in a gas chromatography experiment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 + will become defined class/xps + gas chromatography equipment @@ -19843,13 +20102,13 @@ that has_part some material entity is a material entity. If we add as equivalent - syringe filter + syringe filter - A small membrane filter of defined pore size, that filters samples from a syringe. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 - syringe filter + A small membrane filter of defined pore size, that filters samples from a syringe. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 + syringe filter @@ -19864,14 +20123,14 @@ that has_part some material entity is a material entity. If we add as equivalent - Bruker SampleRail system + Bruker SampleRail system - This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 - NMR instrument - Bruker SampleRail system + This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 + NMR instrument + Bruker SampleRail system @@ -19880,13 +20139,13 @@ that has_part some material entity is a material entity. If we add as equivalent - column compartment + column compartment - For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 - column compartment + For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 + column compartment @@ -19895,13 +20154,13 @@ that has_part some material entity is a material entity. If we add as equivalent - capillary pump system + capillary pump system - A pump system optimized for capillary chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 - capillary pump system + A pump system optimized for capillary chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 + capillary pump system @@ -19916,13 +20175,13 @@ that has_part some material entity is a material entity. If we add as equivalent - evaporative light scattering detector + evaporative light scattering detector - The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 - evaporative light scattering detector + The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 + evaporative light scattering detector @@ -19949,13 +20208,13 @@ that has_part some material entity is a material entity. If we add as equivalent - isolation of PBMCs - cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. + isolation of PBMCs + cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. - a process in which cells with a single nucleus are isolated from a blood sample - PERSON: bjoern peters - wiki http://en.wikipedia.org/wiki/PBMC - isolation of PBMCs + a process in which cells with a single nucleus are isolated from a blood sample + PERSON: bjoern peters + wiki http://en.wikipedia.org/wiki/PBMC + isolation of PBMCs @@ -19964,14 +20223,14 @@ that has_part some material entity is a material entity. If we add as equivalent - column cartridger + column cartridger - A chromatography device where the column cartridge is inserted into and stabilised. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 - check on definition ! - column cartridger + A chromatography device where the column cartridge is inserted into and stabilised. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 + check on definition ! + column cartridger @@ -19980,13 +20239,13 @@ that has_part some material entity is a material entity. If we add as equivalent - nitrogen generator + nitrogen generator - A gas generator that generates nitrogen gas. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 - nitrogen generator + A gas generator that generates nitrogen gas. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 + nitrogen generator @@ -19995,14 +20254,14 @@ that has_part some material entity is a material entity. If we add as equivalent - needle assembly + needle assembly - The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 - chromatography device, check on definition ! - needle assembly + The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 + chromatography device, check on definition ! + needle assembly @@ -20039,18 +20298,18 @@ that has_part some material entity is a material entity. If we add as equivalent - reverse transcribed polymerase chain reaction - Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. + reverse transcribed polymerase chain reaction + Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. - 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation - Philippe Rocca-Serra - RT-PCR - reverse transcription polymerase chain reaction - reverse transcribed polymerase chain reaction + reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. + 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation + Philippe Rocca-Serra + RT-PCR + reverse transcription polymerase chain reaction + reverse transcribed polymerase chain reaction @@ -20059,15 +20318,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker Capillary LC-NMR platform + Bruker Capillary LC-NMR platform - Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 - NMR instrument - hyphenated NMR instrument platform - Bruker Capillary LC-NMR platform + Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 + NMR instrument + hyphenated NMR instrument platform + Bruker Capillary LC-NMR platform @@ -20076,14 +20335,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - gas chromatography oven + gas chromatography oven - A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 - gas chromatography equipment - gas chromatography oven + A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 + gas chromatography equipment + gas chromatography oven @@ -20092,14 +20351,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - autosampler + autosampler - An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 - NMR instrument - autosampler + An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 + NMR instrument + autosampler @@ -20108,13 +20367,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - isocratic pump system + isocratic pump system - A pump system optimized for isocratic chromatography. - PERSON:Daniel Schober - WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 - isocratic pump system + A pump system optimized for isocratic chromatography. + PERSON:Daniel Schober + WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 + isocratic pump system @@ -20123,13 +20382,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - flash pump system + flash pump system - Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 - flash pump system + Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 + flash pump system @@ -20138,14 +20397,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Varian UNITY INOVA spectrometer + Varian UNITY INOVA spectrometer - The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. - PERSON:Daniel Schober - WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 - NMR instrument - Varian UNITY INOVA spectrometer + The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. + PERSON:Daniel Schober + WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 + NMR instrument + Varian UNITY INOVA spectrometer @@ -20154,14 +20413,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - liquid NMR probe + liquid NMR probe - An NMR probe that is designed to hold a liquid sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 - NMR device - liquid NMR probe + An NMR probe that is designed to hold a liquid sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 + NMR device + liquid NMR probe @@ -20170,13 +20429,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - ion exchange column + ion exchange column - An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 - ion exchange column + An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 + ion exchange column @@ -20185,14 +20444,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker NMR probe + Bruker NMR probe - An NMR probe that is manufactured by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 - NMR device, TODO: May need no definition. - Bruker NMR probe + An NMR probe that is manufactured by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 + NMR device, TODO: May need no definition. + Bruker NMR probe @@ -20201,13 +20460,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - anion trap column + anion trap column - An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 - anion trap column + An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 + anion trap column @@ -20222,13 +20481,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - fluorescene detector + fluorescene detector - A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 - fluorescene detector + A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 + fluorescene detector @@ -20237,14 +20496,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - tecmag EAGLE probe + tecmag EAGLE probe - The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 - NMR probe - tecmag EAGLE probe + The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 + NMR probe + tecmag EAGLE probe @@ -20259,13 +20518,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - electrical conductivity detector + electrical conductivity detector - The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 - electrical conductivity detector + The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 + electrical conductivity detector @@ -20280,17 +20539,17 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - NMR instrument + NMR instrument - An Instrument which is used to carry out a NMR analysis of some sample. - PERSON:Daniel Schober - MRI scanner - NMR instrument - magnetic resonance imaging scanner - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 - NMR instrument - NMR instrument + An Instrument which is used to carry out a NMR analysis of some sample. + PERSON:Daniel Schober + MRI scanner + NMR instrument + magnetic resonance imaging scanner + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 + NMR instrument + NMR instrument @@ -20299,14 +20558,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker UltraShield NMR magnet + Bruker UltraShield NMR magnet - An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 - NMR instrument - Bruker UltraShield NMR magnet + An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 + NMR instrument + Bruker UltraShield NMR magnet @@ -20315,13 +20574,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - piston-seal + piston-seal - The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 - piston-seal + The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 + piston-seal @@ -20330,14 +20589,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - mass selective detector + mass selective detector - A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. - PERSON:Daniel Schober - mass spectrometry detector - WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 - mass selective detector + A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. + PERSON:Daniel Schober + mass spectrometry detector + WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 + mass selective detector @@ -20346,13 +20605,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - spin column + spin column - A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 - spin column + A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 + spin column @@ -20380,13 +20639,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - manufacturer role - With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. + manufacturer role + With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. - Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. - GROUP: Role Branch - OBI - manufacturer role + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. + GROUP: Role Branch + OBI + manufacturer role @@ -20395,14 +20654,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - transfer line + transfer line - A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. - PERSON:Daniel Schober - WEB:<http://www.freepatentsonline.com/5702671.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 - chromatography device - transfer line + A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. + PERSON:Daniel Schober + WEB:<http://www.freepatentsonline.com/5702671.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 + chromatography device + transfer line @@ -20411,13 +20670,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - gradient pump system + gradient pump system - A pump system optimized for gradient chromatography. - PERSON:Daniel Schober - WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 - gradient pump system + A pump system optimized for gradient chromatography. + PERSON:Daniel Schober + WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 + gradient pump system @@ -20426,13 +20685,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - high temperature column + high temperature column - A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 - high temperature column + A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 + high temperature column @@ -20441,14 +20700,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker Ultrastabilized NMR magnet + Bruker Ultrastabilized NMR magnet - An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 - NMR instrument - Bruker Ultrastabilized NMR magnet + An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 + NMR instrument + Bruker Ultrastabilized NMR magnet @@ -20469,8 +20728,8 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - scattered molecular aggregate - the sodium and chloride ions in a glass of salt water + scattered molecular aggregate + the sodium and chloride ions in a glass of salt water a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates PERSON: Alan Ruttenberg @@ -20486,11 +20745,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 obsolete_molecular concentration - the phosphate concentration should be 0.1M + the phosphate concentration should be 0.1M - A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. - PERSON: Alan Ruttenberg - Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. + A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. + PERSON: Alan Ruttenberg + Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. obsolete_molecular concentration true @@ -20508,14 +20767,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - NMR sample tube + NMR sample tube - The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 - NMR device - NMR sample tube + The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 + NMR device + NMR sample tube @@ -20524,14 +20783,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Varian UNITY spectrometer + Varian UNITY spectrometer - The predecessor series of the Varian UNITY INOVA spectrometer. - PERSON:Daniel Schober - WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 - NMR instrument - Varian UNITY spectrometer + The predecessor series of the Varian UNITY INOVA spectrometer. + PERSON:Daniel Schober + WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 + NMR instrument + Varian UNITY spectrometer @@ -20540,14 +20799,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - AVANCE II spectrometer + AVANCE II spectrometer - A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. - PERSON:Daniel Schober - WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 - NMR instrument - AVANCE II spectrometer + A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. + PERSON:Daniel Schober + WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 + NMR instrument + AVANCE II spectrometer @@ -20556,13 +20815,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - y-column connector + y-column connector - A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 - y-column connector + A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 + y-column connector @@ -20571,15 +20830,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker LC-NMR/MS platform + Bruker LC-NMR/MS platform - Includes the connection to a high-resolution TOF-LC-MS system. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 - NMR instrument - hyphenated NMR instrument platform - Bruker LC-NMR/MS platform + Includes the connection to a high-resolution TOF-LC-MS system. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 + NMR instrument + hyphenated NMR instrument platform + Bruker LC-NMR/MS platform @@ -20594,13 +20853,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - refractive index detector + refractive index detector - For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 - refractive index detector + For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 + refractive index detector @@ -20609,13 +20868,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - anion exchange column + anion exchange column - An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 - anion exchange column + An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 + anion exchange column @@ -20624,13 +20883,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - plunger column + plunger column - A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 - plunger column + A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 + plunger column @@ -20639,14 +20898,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - flame photometric detector + flame photometric detector - The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. - PERSON:Daniel Schober - FPD - WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 - flame photometric detector + The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. + PERSON:Daniel Schober + FPD + WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 + flame photometric detector @@ -20655,13 +20914,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - chromatography pump system + chromatography pump system - Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). - PERSON:Daniel Schober - WEB:<http://en.wikipedia.org/wiki/Column_chromatography> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 - chromatography pump system + Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). + PERSON:Daniel Schober + WEB:<http://en.wikipedia.org/wiki/Column_chromatography> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 + chromatography pump system @@ -20670,14 +20929,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker 1mm MicroProbe + Bruker 1mm MicroProbe - Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 - NMR probe - Bruker 1mm MicroProbe + Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 + NMR probe + Bruker 1mm MicroProbe @@ -20686,15 +20945,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker BEST NMR system + Bruker BEST NMR system - The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. - PERSON:Daniel Schober - Bruker Efficient Sample Transfer NMR - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 - NMR instrument - Bruker BEST NMR system + The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. + PERSON:Daniel Schober + Bruker Efficient Sample Transfer NMR + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 + NMR instrument + Bruker BEST NMR system @@ -20703,13 +20962,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - chromatography detector filter + chromatography detector filter - An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 - chromatography detector filter + An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 + chromatography detector filter @@ -20718,13 +20977,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - cation trap column + cation trap column - A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 - cation trap column + A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 + cation trap column @@ -20733,14 +20992,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - column adapter + column adapter - An Adapter that enabled the connection of a column to additional devices. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 - chromatography device - column adapter + An Adapter that enabled the connection of a column to additional devices. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 + chromatography device + column adapter @@ -20755,14 +21014,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - pulsed amperometric detector + pulsed amperometric detector - A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). - PERSON:Daniel Schober - PAD - WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 - pulsed amperometric detector + A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). + PERSON:Daniel Schober + PAD + WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 + pulsed amperometric detector @@ -20771,14 +21030,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker NMR instrument + Bruker NMR instrument - An NMR instrument that is manufactured by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 - NMR instrument - Bruker NMR instrument + An NMR instrument that is manufactured by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 + NMR instrument + Bruker NMR instrument @@ -20787,14 +21046,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker NMR magnet + Bruker NMR magnet - An NMR magnet that is manufactured by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 - NMR instrument - Bruker NMR magnet + An NMR magnet that is manufactured by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 + NMR instrument + Bruker NMR magnet @@ -20803,13 +21062,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - ozone-induced chemiluminescence detector + ozone-induced chemiluminescence detector - Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. - PERSON:Daniel Schober - WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 - ozone-induced chemiluminescence detector + Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. + PERSON:Daniel Schober + WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 + ozone-induced chemiluminescence detector @@ -20818,14 +21077,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - tecmag NMR console + tecmag NMR console - An NMR console manufactured by tecmac. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 - NMR instrument - tecmag NMR console + An NMR console manufactured by tecmac. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 + NMR instrument + tecmag NMR console @@ -20834,14 +21093,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - JEOL NMR instrument + JEOL NMR instrument - An NMR instrument that is manufactured by JEOL. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 - NMR instrument - JEOL NMR instrument + An NMR instrument that is manufactured by JEOL. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 + NMR instrument + JEOL NMR instrument @@ -20850,14 +21109,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - chromatography consumable + chromatography consumable - A chromatography consumable is a consumable that is used in a chromatography experiment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 - chromatography device - chromatography consumable + A chromatography consumable is a consumable that is used in a chromatography experiment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 + chromatography device + chromatography consumable @@ -20866,14 +21125,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - column frit + column frit - A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/radial/columns.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 - chromatography device - column frit + A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/radial/columns.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 + chromatography device + column frit @@ -20882,13 +21141,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - liquid chromatography column + liquid chromatography column - A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 - liquid chromatography column + A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 + liquid chromatography column @@ -20897,13 +21156,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - detector lamp + detector lamp - A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 - detector lamp + A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 + detector lamp @@ -20912,14 +21171,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - chart recorder + chart recorder - The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 - chromatography device - chart recorder + The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 + chromatography device + chart recorder @@ -20928,13 +21187,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - open tubular column + open tubular column - An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. - PERSON:Daniel Schober - WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 - open tubular column + An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. + PERSON:Daniel Schober + WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 + open tubular column @@ -20943,15 +21202,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - high resolution magic angle spin probe + high resolution magic angle spin probe - Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. - PERSON:Daniel Schober - high resolution MAS, hr-MAS - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 - NMR probe - high resolution magic angle spin probe + Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. + PERSON:Daniel Schober + high resolution MAS, hr-MAS + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 + NMR probe + high resolution magic angle spin probe @@ -20960,13 +21219,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - hydrogen generator + hydrogen generator - A gas generator that generates hydrogen gas. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 - hydrogen generator + A gas generator that generates hydrogen gas. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 + hydrogen generator @@ -20975,13 +21234,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - glass column + glass column - A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 - glass column + A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 + glass column @@ -20990,13 +21249,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - auto injector + auto injector - A gas chromatography device that can auto-inject a small number of samples an inlet. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 - auto injector + A gas chromatography device that can auto-inject a small number of samples an inlet. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 + auto injector @@ -21005,14 +21264,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Varian NMR instrument + Varian NMR instrument - An NMR instrument that is manufactured by Varian. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 - NMR instrument - Varian NMR instrument + An NMR instrument that is manufactured by Varian. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 + NMR instrument + Varian NMR instrument @@ -21021,15 +21280,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker MATCH tube holder system + Bruker MATCH tube holder system - The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. - PERSON:Daniel Schober - Bruker Multiple Adjustable Tube Clamp Holder - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 - NMR instrument - Bruker MATCH tube holder system + The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. + PERSON:Daniel Schober + Bruker Multiple Adjustable Tube Clamp Holder + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 + NMR instrument + Bruker MATCH tube holder system @@ -21038,15 +21297,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker SPE-NMR platform + Bruker SPE-NMR platform - A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 - NMR instrument - hyphenated NMR instrument platform - Bruker SPE-NMR platform + A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 + NMR instrument + hyphenated NMR instrument platform + Bruker SPE-NMR platform @@ -21055,14 +21314,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - guard column + guard column - Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 - chromatography device - guard column + Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 + chromatography device + guard column @@ -21124,12 +21383,12 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 protein expression profiling assay - Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203 + Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203 - An assay that determines protein expression and translation activity using protein extracts collected from a material entity. - Phlippe Rocca-Serra - proteomic analysis - OBI branch derived + An assay that determines protein expression and translation activity using protein extracts collected from a material entity. + Phlippe Rocca-Serra + proteomic analysis + OBI branch derived protein expression profiling assay @@ -21139,15 +21398,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - high resolution probe with automatic tuning and matching + high resolution probe with automatic tuning and matching - The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. - PERSON:Daniel Schober - High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 - NMR probe - high resolution probe with automatic tuning and matching + The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. + PERSON:Daniel Schober + High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 + NMR probe + high resolution probe with automatic tuning and matching @@ -21156,13 +21415,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - fluorine-induced chemiluminescence detector + fluorine-induced chemiluminescence detector - A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. - PERSON:Daniel Schober - WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 - fluorine-induced chemiluminescence detector + A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. + PERSON:Daniel Schober + WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 + fluorine-induced chemiluminescence detector @@ -21171,13 +21430,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - size exclusion column + size exclusion column - A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 - size exclusion column + A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 + size exclusion column @@ -21186,14 +21445,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - chromatography splitter + chromatography splitter - An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 - chromatography device - chromatography splitter + An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 + chromatography device + chromatography splitter @@ -21202,14 +21461,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker micro imaging probe + Bruker micro imaging probe - For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/probes_microimaging.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 - NMR probe - Bruker micro imaging probe + For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/probes_microimaging.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 + NMR probe + Bruker micro imaging probe @@ -21218,13 +21477,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - custom made column + custom made column - A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 - custom made column + A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 + custom made column @@ -21233,13 +21492,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - gel permeation column + gel permeation column - A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. - PERSON:Daniel Schober - WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 - gel permeation column + A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. + PERSON:Daniel Schober + WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 + gel permeation column @@ -21249,12 +21508,12 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 NMR spectroscopy assay - Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 + Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 - An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. - Philippe Rocca-Serra - Nuclear magnetic resonance spectroscopy - url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy + An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. + Philippe Rocca-Serra + Nuclear magnetic resonance spectroscopy + url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy NMR spectroscopy assay @@ -21264,14 +21523,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker SampleJet system + Bruker SampleJet system - Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 - NMR instrument - Bruker SampleJet system + Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 + NMR instrument + Bruker SampleJet system @@ -21280,14 +21539,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - JEOL ECX NMR spectrometer + JEOL ECX NMR spectrometer - The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. - PERSON:Daniel Schober - WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 - NMR instrument - JEOL ECX NMR spectrometer + The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. + PERSON:Daniel Schober + WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 + NMR instrument + JEOL ECX NMR spectrometer @@ -21362,12 +21621,12 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 DNA sequencing assay - Illumina (Solexa) sequencing is an example of DNA sequencing + Illumina (Solexa) sequencing is an example of DNA sequencing - A sequencing assay which determines information on the sequence of a DNA molecule. - Philippe Rocca-Serra - nucleotide sequencing - url:https://en.wikipedia.org/wiki/DNA_sequencing + A sequencing assay which determines information on the sequence of a DNA molecule. + Philippe Rocca-Serra + nucleotide sequencing + url:https://en.wikipedia.org/wiki/DNA_sequencing DNA sequencing assay @@ -21377,13 +21636,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - quaternary pump system + quaternary pump system - A pump system that pump and mix up to four different solvents in parallel. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 - quaternary pump system + A pump system that pump and mix up to four different solvents in parallel. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 + quaternary pump system @@ -21392,13 +21651,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - carbon nanotube column + carbon nanotube column - Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. - PERSON:Daniel Schober - WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 - carbon nanotube column + Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. + PERSON:Daniel Schober + WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 + carbon nanotube column @@ -21407,15 +21666,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker solid magic angle spinning probe + Bruker solid magic angle spinning probe - Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. - PERSON:Daniel Schober - solid MAS probe - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 - NMR probe - Bruker solid magic angle spinning probe + Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. + PERSON:Daniel Schober + solid MAS probe + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 + NMR probe + Bruker solid magic angle spinning probe @@ -21441,13 +21700,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 hematology assay - Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 + Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments - Philippe Rocca-Serra - blood analysis - haematology - OBI branch derived + An assay that studies blood and blood producing organs using a variety of techniques and instruments + Philippe Rocca-Serra + blood analysis + haematology + OBI branch derived hematology assay @@ -21457,14 +21716,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Varian MERCURY spectrometer + Varian MERCURY spectrometer - MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. - PERSON:Daniel Schober - WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 - NMR instrument - Varian MERCURY spectrometer + MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. + PERSON:Daniel Schober + WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 + NMR instrument + Varian MERCURY spectrometer @@ -21473,15 +21732,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Bruker Metabolic Profiler + Bruker Metabolic Profiler - An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 - NMR instrument - hyphenated NMR instrument platform - Bruker Metabolic Profiler + An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 + NMR instrument + hyphenated NMR instrument platform + Bruker Metabolic Profiler @@ -21490,13 +21749,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - column heater + column heater - The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 - column heater + The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 + column heater @@ -21579,12 +21838,12 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 DNA methylation profiling assay - Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 + Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 - An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. - Philippe Rocca-Serra - DNA methylation profiling - OBI branch derived + An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. + Philippe Rocca-Serra + DNA methylation profiling + OBI branch derived DNA methylation profiling assay @@ -21594,14 +21853,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - JEOL CapNMR probe + JEOL CapNMR probe - The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. - PERSON:Daniel Schober - WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 - NMR probe - JEOL CapNMR probe + The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. + PERSON:Daniel Schober + WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 + NMR probe + JEOL CapNMR probe @@ -21616,14 +21875,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - acquisition computer + acquisition computer - A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 - NMR instrument - acquisition computer + A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 + NMR instrument + acquisition computer @@ -21632,15 +21891,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - gas chromatography detector + gas chromatography detector - A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. - PERSON:Daniel Schober - FID - WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 - chromatography detector, defined class/xps - gas chromatography detector + A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. + PERSON:Daniel Schober + FID + WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 + chromatography detector, defined class/xps + gas chromatography detector @@ -21649,14 +21908,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - gas purifier + gas purifier - Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. - PERSON:Daniel Schober - WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 - gas chromatography equipment - gas purifier + Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. + PERSON:Daniel Schober + WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 + gas chromatography equipment + gas purifier @@ -21673,13 +21932,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - material separation objective - The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. + material separation objective + The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. - is an objective to transform a material entity into spatially separated components. - PPPB branch - PPPB branch - material separation objective + is an objective to transform a material entity into spatially separated components. + PPPB branch + PPPB branch + material separation objective @@ -21688,14 +21947,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - indirect detection probe + indirect detection probe - An NMR probe designed to allow the indirect detection of acquisition nuclei. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 - NMR device - indirect detection probe + An NMR probe designed to allow the indirect detection of acquisition nuclei. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 + NMR device + indirect detection probe @@ -21704,14 +21963,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - JEOL ECA NMR spectrometer + JEOL ECA NMR spectrometer - The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. - PERSON:Daniel Schober - WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 - NMR instrument - JEOL ECA NMR spectrometer + The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. + PERSON:Daniel Schober + WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 + NMR instrument + JEOL ECA NMR spectrometer @@ -21720,14 +21979,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - atomic emission detector + atomic emission detector - Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. - PERSON:Daniel Schober - AED - WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 - atomic emission detector + Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. + PERSON:Daniel Schober + AED + WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 + atomic emission detector @@ -21742,14 +22001,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - clustered data set - A clustered data set is the output of a K means clustering data transformation + clustered data set + A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. - PERSON: James Malone - PERSON: Monnie McGee - data set with assigned discovered class labels - AR thinks could be a data item instead + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned discovered class labels + AR thinks could be a data item instead clustered data set @@ -21765,11 +22024,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - data set of features + data set of features A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. - PERSON: James Malone - PERSON: Monnie McGee + PERSON: James Malone + PERSON: Monnie McGee data set of features @@ -21820,13 +22079,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - urine specimen + urine specimen - a portion of urine collected from an organism - 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. - This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active - are we happy calling collection of urine a material separation? - urine specimen + a portion of urine collected from an organism + 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. + This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active + are we happy calling collection of urine a material separation? + urine specimen @@ -21853,14 +22112,14 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - material combination - Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. + material combination + Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. - is a material processing with the objective to combine two or more material entities as input into a single material entity as output. - created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. - bp - bp - material combination + is a material processing with the objective to combine two or more material entities as input into a single material entity as output. + created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. + bp + bp + material combination @@ -21873,8 +22132,8 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. James Malone - PERSON: James Malone - PERSON: Ryan Brinkman + PERSON: James Malone + PERSON: Ryan Brinkman fuzzy clustering objective @@ -21890,13 +22149,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - device setting - Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification + device setting + Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification - a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device + a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 - PERSON: Frank Gibson - device setting + PERSON: Frank Gibson + device setting @@ -21923,13 +22182,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - blood specimen - blood drawn from a human for glucose assay + blood specimen + blood drawn from a human for glucose assay - a material entity derived from a portion of blood collected from an organism - Bjoern Peters - Bjoern Peters - blood specimen + a material entity derived from a portion of blood collected from an organism + Bjoern Peters + Bjoern Peters + blood specimen @@ -21944,11 +22203,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - data set of predicted values according to fitted curve + data set of predicted values according to fitted curve A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. - PERSON: James Malone - PERSON: Monnie McGee + PERSON: James Malone + PERSON: Monnie McGee data set of predicted values according to fitted curve @@ -21958,18 +22217,18 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - data representational model - gene regulatory graph model - phylogenetic tree - protein interaction network + data representational model + gene regulatory graph model + phylogenetic tree + protein interaction network - Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. - Melanie Courtot - data structure - data structure specification - GROUP: OBI - 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 - data representational model + Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. + Melanie Courtot + data structure + data structure specification + GROUP: OBI + 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 + data representational model @@ -22004,16 +22263,16 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation - A planned process with the objective of collecting a specimen. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ - Bjoern Peters + Bjoern Peters specimen collection - 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession - 6/9/09: used at workshop + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop specimen collection process @@ -22029,11 +22288,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - background corrected data set + background corrected data set A data set that is produced as the output of a background correction data transformation. - PERSON: James Malone - PERSON: Melanie Courtot + PERSON: James Malone + PERSON: Melanie Courtot background corrected data set @@ -22068,12 +22327,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ enzyme-linked immunosorbent assay - 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. + 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. - An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. - IEDB - ELISA - IEDB + An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. + IEDB + ELISA + IEDB enzyme-linked immunosorbent assay @@ -22089,11 +22348,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - error corrected data set + error corrected data set A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). - PERSON: James Malone - PERSON: Monnie McGee + PERSON: James Malone + PERSON: Monnie McGee error corrected data set @@ -22120,8 +22379,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. - James Malone - supervised classification data transformation + James Malone + supervised classification data transformation PERSON: James Malone class prediction data transformation @@ -22157,11 +22416,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ BrdU incorporation assay - The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. + The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. - A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. - IEDB - IEDB + A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. + IEDB + IEDB BrdU incorporation assay @@ -22172,16 +22431,16 @@ http://sourceforge.net/p/obi/obi-terms/716/ obsolete intracellular cytokine staining assay - Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies + Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies - The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. - IEDB - ICCS - ICS - IEDB + The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. + IEDB + ICCS + ICS + IEDB - intracellular cytokine staining (ICS) + intracellular cytokine staining (ICS) obsolete intracellular cytokine staining assay true @@ -22209,7 +22468,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ background correction data transformation A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. - James Malone + James Malone PERSON: James Malone background correction data transformation @@ -22221,15 +22480,15 @@ http://sourceforge.net/p/obi/obi-terms/716/ obsolete MHC multimer staining assay - Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. + Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. - An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer - IEDB - MHC tetramer assay - IEDB + An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer + IEDB + MHC tetramer assay + IEDB - MHC tetramer/multimer staining + MHC tetramer/multimer staining obsolete MHC multimer staining assay true @@ -22250,8 +22509,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. James Malone - Monnie McGee - EDITORS + Monnie McGee + EDITORS error correction data transformation @@ -22292,11 +22551,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ tritiated thymidine incorporation assay - The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. + The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. - A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. - IEDB - IEDB + A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. + IEDB + IEDB tritiated thymidine incorporation assay @@ -22327,12 +22586,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - sample from organism + sample from organism - a material obtained from an organism in order to be a representative of the whole - 5/29: This is a helper class for now - we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. - sample from organism + a material obtained from an organism in order to be a representative of the whole + 5/29: This is a helper class for now + we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. + sample from organism @@ -22350,7 +22609,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ statistical hypothesis test A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. - James Malone + James Malone PERSON: James Malone statistical hypothesis test @@ -22367,12 +22626,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - center value + center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - median + PERSON: James Malone + PERSON: Monnie McGee + median center value @@ -22384,11 +22643,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ statistical hypothesis test objective - is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation + is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation James Malone - Person:Helen Parkinson - hypothesis test objective - WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing + Person:Helen Parkinson + hypothesis test objective + WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing statistical hypothesis test objective @@ -22404,11 +22663,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - reduced dimension data set + reduced dimension data set A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. - PERSON: James Malone - PERSON: Monnie McGee + PERSON: James Malone + PERSON: Monnie McGee reduced dimension data set @@ -22419,11 +22678,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - portioning objective - The objective to obtain multiple aliquots of an enzyme preparation. + portioning objective + The objective to obtain multiple aliquots of an enzyme preparation. - A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. - portioning objective + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. + portioning objective @@ -22438,12 +22697,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - average value + average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - arithmetic mean + PERSON: James Malone + PERSON: Monnie McGee + arithmetic mean average value @@ -22476,12 +22735,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - whole organism preparation - putting a mouse in the blender. Not: putting a mouse on a scale + whole organism preparation + putting a mouse in the blender. Not: putting a mouse on a scale - A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained - does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. - whole organism preparation + A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained + does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. + whole organism preparation @@ -22490,12 +22749,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - separation into different composition objective - The objective to obtain cells contained in a sample of blood. + separation into different composition objective + The objective to obtain cells contained in a sample of blood. - A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). - We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives - separation into different composition objective + A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). + We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives + separation into different composition objective @@ -22506,8 +22765,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ obsolete_study result - Study result is an information content entity that is a specified data output of a study. - GROUP: OBI + Study result is an information content entity that is a specified data output of a study. + GROUP: OBI obsolete_study result true @@ -22520,11 +22779,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective - The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. - Bjoern Peters - Bjoern Peters + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters specimen collection objective @@ -22558,13 +22817,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - creating a mixture of molecules in solution - The production of PBS + creating a mixture of molecules in solution + The production of PBS - is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. - Bjoern Peters - PERSON: Helen Parkinson - creating a mixture of molecules in solution + is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. + Bjoern Peters + PERSON: Helen Parkinson + creating a mixture of molecules in solution @@ -22573,12 +22832,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - material combination objective + material combination objective - is an objective to obtain an output material that contains several input materials. - PPPB branch - bp - material combination objective + is an objective to obtain an output material that contains several input materials. + PPPB branch + bp + material combination objective @@ -22587,12 +22846,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - nucleotide overhang cloning - Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs + nucleotide overhang cloning + Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs - Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation - Helen Parkinson - nucleotide overhang cloning + Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation + Helen Parkinson + nucleotide overhang cloning @@ -22601,13 +22860,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - rodent care protocol - Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. + rodent care protocol + Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. - A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. - Bjoern Peters - Bjoern Peters - rodent care protocol + A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. + Bjoern Peters + Bjoern Peters + rodent care protocol @@ -22622,13 +22881,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - 454 Genome Sequence 20 - PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. + 454 Genome Sequence 20 + PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. - is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. - Philippe Rocca-Serra - GS 20 - 454 Genome Sequence 20 + is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. + Philippe Rocca-Serra + GS 20 + 454 Genome Sequence 20 @@ -22649,13 +22908,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - immunoprecipitation - PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. + immunoprecipitation + PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. - is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity - Philippe Rocca-Serra - OBI plan and planned process branch - immunoprecipitation + is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity + Philippe Rocca-Serra + OBI plan and planned process branch + immunoprecipitation @@ -22670,12 +22929,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - ABI 377 automated sequencer + ABI 377 automated sequencer - is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. - Philippe Rocca-Serra - Applied Biosystems - ABI 377 automated sequencer + is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. + Philippe Rocca-Serra + Applied Biosystems + ABI 377 automated sequencer @@ -22684,10 +22943,10 @@ http://sourceforge.net/p/obi/obi-terms/716/ - recombination enzyme based cloning + recombination enzyme based cloning - a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector - recombination enzyme based cloning + a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector + recombination enzyme based cloning @@ -22846,12 +23105,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ MeDIP-seq assay - PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. + PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. - A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. - Philippe Rocca-Serra - Methylated DNA immunoprecipitation sequencing assay - url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation + A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. + Philippe Rocca-Serra + Methylated DNA immunoprecipitation sequencing assay + url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation MeDIP-seq assay @@ -22879,14 +23138,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - animal feeding - giving crickets to a snake. + animal feeding + giving crickets to a snake. - animal feeding is a process in which animals are provided with food - In an investigation, this will typically be part of an animal care process - Bjoern Peters - branch derived - animal feeding + animal feeding is a process in which animals are provided with food + In an investigation, this will typically be part of an animal care process + Bjoern Peters + branch derived + animal feeding @@ -22940,13 +23199,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ chain termination sequencing assay - PMID: 271968. DNA sequencing with chain-terminating inhibitors. + PMID: 271968. DNA sequencing with chain-terminating inhibitors. - A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position - Philippe Rocca-Serra - Sanger sequencing - dye terminator sequencing - url:https://en.wikipedia.org/wiki/Sanger_sequencing + A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position + Philippe Rocca-Serra + Sanger sequencing + dye terminator sequencing + url:https://en.wikipedia.org/wiki/Sanger_sequencing chain termination sequencing assay @@ -22962,13 +23221,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - AB SOLiD System - PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. + AB SOLiD System + PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. - is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation - Philippe Rocca-Serra - Applied Biosystems - AB SOLiD System + is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation + Philippe Rocca-Serra + Applied Biosystems + AB SOLiD System @@ -23002,12 +23261,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ Helicos sequencing assay - PMID: 18388294. Single-molecule DNA sequencing of a viral genome. + PMID: 18388294. Single-molecule DNA sequencing of a viral genome. - A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. - Philippe Rocca-Serra - true single molecule sequencing - url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing + A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. + Philippe Rocca-Serra + true single molecule sequencing + url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing Helicos sequencing assay @@ -23019,9 +23278,9 @@ http://sourceforge.net/p/obi/obi-terms/716/ obsolete_DNA ligase - A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule - Kevin Clancy, Bjoern Peters - ligase + A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule + Kevin Clancy, Bjoern Peters + ligase obsolete_DNA ligase true @@ -23058,7 +23317,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ survival assessment assay - An assay that measures the occurrence of death events in one or more organisms over time + An assay that measures the occurrence of death events in one or more organisms over time survival assessment assay @@ -23074,14 +23333,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - support vector machine + support vector machine - A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. - James Malone - Ryan Brinkman - SVM - PERSON: Ryan Brinkman - support vector machine + A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. + James Malone + Ryan Brinkman + SVM + PERSON: Ryan Brinkman + support vector machine @@ -23112,14 +23371,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - self-organizing map + self-organizing map - A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. - James Malone - Ryan Brinkman - SOM - PERSON: Ryan Brinkman - self-organizing map + A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. + James Malone + Ryan Brinkman + SOM + PERSON: Ryan Brinkman + self-organizing map @@ -23134,15 +23393,15 @@ http://sourceforge.net/p/obi/obi-terms/716/ - 454 Genome Sequencer FLX - PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. + 454 Genome Sequencer FLX + PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. - is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. - Philippe Rocca-Serra - 454 GS FLX - GS-FLX - adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay - 454 Genome Sequencer FLX + is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + Philippe Rocca-Serra + 454 GS FLX + GS-FLX + adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay + 454 Genome Sequencer FLX @@ -23157,13 +23416,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - Illumina Genome Analyzer II - PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. + Illumina Genome Analyzer II + PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. - is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology - Philippe Rocca-Serra - Illumina Corporation - Illumina Genome Analyzer II + is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + Philippe Rocca-Serra + Illumina Corporation + Illumina Genome Analyzer II @@ -23172,11 +23431,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - decision tree induction objective + decision tree induction objective - A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. - James Malone - decision tree induction objective + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + James Malone + decision tree induction objective @@ -23227,11 +23486,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ Edman degradation - Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. + Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. - A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. - IEDB - IEDB + A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. + IEDB + IEDB Edman degradation @@ -23280,11 +23539,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ SOLiD sequencing assay - PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. + PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. - A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. - Philippe Rocca-Serra - url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing + A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. + Philippe Rocca-Serra + url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing SOLiD sequencing assay @@ -23303,7 +23562,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. - James Malone + James Malone PERSON: James Malone decision tree building data transformation @@ -23341,10 +23600,10 @@ http://sourceforge.net/p/obi/obi-terms/716/ - laboratory animal care + laboratory animal care - a process that realizes an animal care protocol that specifies how animals are kept and maintained - laboratory animal care + a process that realizes an animal care protocol that specifies how animals are kept and maintained + laboratory animal care @@ -23360,13 +23619,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - yeast artificial chromosome vector + yeast artificial chromosome vector - a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences - this should be a child of 'chromosome' if we import that from another source - Kevin Clancy, Bjoern Peters - YAC - yeast artificial chromosome vector + a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences + this should be a child of 'chromosome' if we import that from another source + Kevin Clancy, Bjoern Peters + YAC + yeast artificial chromosome vector @@ -23381,12 +23640,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - Li-Cor 4300 DNA Analysis System + Li-Cor 4300 DNA Analysis System - is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing - Philippe Rocca-Serra - OBI and Li-Cor - Li-Cor 4300 DNA Analysis System + is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing + Philippe Rocca-Serra + OBI and Li-Cor + Li-Cor 4300 DNA Analysis System @@ -23429,13 +23688,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - library preparation - PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. + library preparation + PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. - is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. - Philippe Rocca-Serra - library construction - library preparation + is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. + Philippe Rocca-Serra + library construction + library preparation @@ -23502,10 +23761,10 @@ http://sourceforge.net/p/obi/obi-terms/716/ - pathogen challenge + pathogen challenge - A pathogen challenge is the administration of a live pathogenic organism to a host - pathogen challenge + A pathogen challenge is the administration of a live pathogenic organism to a host + pathogen challenge @@ -23514,13 +23773,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - GenePattern software + GenePattern software - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. - James Malone - Person:Helen Parkinson - WEB: http://www.broadinstitute.org/cancer/software/genepattern/ - GenePattern software + a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + James Malone + Person:Helen Parkinson + WEB: http://www.broadinstitute.org/cancer/software/genepattern/ + GenePattern software @@ -23529,15 +23788,15 @@ http://sourceforge.net/p/obi/obi-terms/716/ - graph of vertices - For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. + graph of vertices + For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. - A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. - Bjoern Peters - Chris Stoeckert - James Malone - WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html - graph of vertices + A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. + Bjoern Peters + Chris Stoeckert + James Malone + WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html + graph of vertices @@ -23546,13 +23805,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - animal care protocol - Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. + animal care protocol + Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. - An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes - Bjoern Peters - Bjoern Peters - animal care protocol + An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes + Bjoern Peters + Bjoern Peters + animal care protocol @@ -23595,13 +23854,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ ChIP-seq assay - PMID: 19275939 + PMID: 19275939 - An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin - Bjoern Peters - Philippe Rocca-Serra - chromatin immunoprecipitation sequencing assay - url:https://en.wikipedia.org/wiki/ChIP-sequencing + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin + Bjoern Peters + Philippe Rocca-Serra + chromatin immunoprecipitation sequencing assay + url:https://en.wikipedia.org/wiki/ChIP-sequencing ChIP-seq assay @@ -23617,11 +23876,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - HeliScope Single Molecule Sequencer + HeliScope Single Molecule Sequencer - is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry - Philippe Rocca-Serra - HeliScope Single Molecule Sequencer + is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry + Philippe Rocca-Serra + HeliScope Single Molecule Sequencer @@ -23642,14 +23901,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - pathogen role - Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383 + pathogen role + Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383 - pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role - GROUP: Role Branch - OBI - 6 April 2009: from the Vaccine Community - pathogen role + pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role + GROUP: Role Branch + OBI + 6 April 2009: from the Vaccine Community + pathogen role @@ -23664,12 +23923,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - vaccine preparation - The production of B. pertussis vaccine. + vaccine preparation + The production of B. pertussis vaccine. - vaccine preparation is a planned process with specified output a vaccine - OBI - vaccine preparation + vaccine preparation is a planned process with specified output a vaccine + OBI + vaccine preparation @@ -23684,17 +23943,17 @@ http://sourceforge.net/p/obi/obi-terms/716/ - immunologic adjuvant role - Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant + immunologic adjuvant role + Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant - The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. - 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. + The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. + 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'. - GROUP: Role branch - Vaccine Ontology, Wikipedia, OBI - Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 - - immunologic adjuvant role + GROUP: Role branch + Vaccine Ontology, Wikipedia, OBI + Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 + + immunologic adjuvant role @@ -23767,11 +24026,11 @@ the role 'adjuvant role' inheres in some 'material entity' a glucose tolerance test - PMID: 19527607 + PMID: 19527607 - An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. - Philippe Rocca-Serra - NuGO OBI plan branch + An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. + Philippe Rocca-Serra + NuGO OBI plan branch glucose tolerance test @@ -23781,15 +24040,15 @@ the role 'adjuvant role' inheres in some 'material entity' a - paired-end library - PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. + paired-end library + PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. - is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs - Philippe Rocca-Serra - mate-paired library - paired-end tag (PET) library - adapted from information provided by Solid web site - paired-end library + is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs + Philippe Rocca-Serra + mate-paired library + paired-end tag (PET) library + adapted from information provided by Solid web site + paired-end library @@ -23805,11 +24064,11 @@ the role 'adjuvant role' inheres in some 'material entity' a DNA sequencing by ligation assay - ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). + ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). - A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase - Philippe Rocca-Serra - url:https://en.wikipedia.org/wiki/Sequencing_by_ligation + A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase + Philippe Rocca-Serra + url:https://en.wikipedia.org/wiki/Sequencing_by_ligation DNA sequencing by ligation assay @@ -23857,12 +24116,12 @@ the role 'adjuvant role' inheres in some 'material entity' a Solexa sequencing assay - PMID: 18987734 + PMID: 18987734 - A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. - Philippe Rocca-Serra - reversible terminator sequencing - Solexa web site (SS_DNAsequencing.pdf document available on july 2009) + A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. + Philippe Rocca-Serra + reversible terminator sequencing + Solexa web site (SS_DNAsequencing.pdf document available on july 2009) Solexa sequencing assay @@ -23878,16 +24137,16 @@ the role 'adjuvant role' inheres in some 'material entity' a - host role - In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 + host role + In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 - host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role - 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition - GROUP: Role Branch - 30 Mar09 submitted by vaccine community - OBI - http://en.wikipedia.org/wiki/Host_(biology) - host role + host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role + 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition + GROUP: Role Branch + 30 Mar09 submitted by vaccine community + OBI + http://en.wikipedia.org/wiki/Host_(biology) + host role @@ -23896,13 +24155,13 @@ the role 'adjuvant role' inheres in some 'material entity' a - peak matching + peak matching - Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold - James Malone - Ryan Brinkman - PERSON: Ryan Brinkman - peak matching + Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold + James Malone + Ryan Brinkman + PERSON: Ryan Brinkman + peak matching @@ -23937,7 +24196,7 @@ the role 'adjuvant role' inheres in some 'material entity' a A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone - k-NN + k-NN PERSON: James Malone k-nearest neighbors @@ -23993,13 +24252,13 @@ the role 'adjuvant role' inheres in some 'material entity' a - rodent care - keeping animal + rodent care + keeping animal - rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. - PPPB branch - PPPB branch - rodent care + rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. + PPPB branch + PPPB branch + rodent care @@ -24020,11 +24279,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - cloning plasmid + cloning plasmid - A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. - Note: 'cloning vector role' is really a function. Should be dealt with globally - cloning plasmid + A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. + Note: 'cloning vector role' is really a function. Should be dealt with globally + cloning plasmid @@ -24072,11 +24331,11 @@ the role 'adjuvant role' inheres in some 'material entity' a pyrosequencing assay - Pyrosequencing sheds light on DNA sequencing. PMID:1115661 + Pyrosequencing sheds light on DNA sequencing. PMID:1115661 - A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. - Philippe Rocca-Serra - url:http://en.wikipedia.org/wiki/Pyrosequencing + A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. + Philippe Rocca-Serra + url:http://en.wikipedia.org/wiki/Pyrosequencing pyrosequencing assay @@ -24097,10 +24356,10 @@ the role 'adjuvant role' inheres in some 'material entity' a - recombinant vector + recombinant vector - A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. - recombinant vector + A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. + recombinant vector @@ -24115,13 +24374,13 @@ the role 'adjuvant role' inheres in some 'material entity' a - restriction enzyme - The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG + restriction enzyme + The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG - an enzyme that has a specific target cleavage sites within nucleic acids - Kevin Clancy, Bjoern Peters - 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments - restriction enzyme + an enzyme that has a specific target cleavage sites within nucleic acids + Kevin Clancy, Bjoern Peters + 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments + restriction enzyme @@ -24137,11 +24396,11 @@ the role 'adjuvant role' inheres in some 'material entity' a DNA sequencing by synthesis assay - Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing + Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing - A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. - Philippe Rocca-Serra - url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html + A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. + Philippe Rocca-Serra + url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html DNA sequencing by synthesis assay @@ -24163,11 +24422,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - NTP-2000 + NTP-2000 - a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents - Jennifer Fostel, Bjoern Peters - NTP-2000 + a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents + Jennifer Fostel, Bjoern Peters + NTP-2000 @@ -24176,12 +24435,12 @@ the role 'adjuvant role' inheres in some 'material entity' a - single fragment library + single fragment library - is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs - Philippe Rocca-Serra - fragment library - single fragment library + is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs + Philippe Rocca-Serra + fragment library + single fragment library @@ -24208,10 +24467,10 @@ the role 'adjuvant role' inheres in some 'material entity' a - cloning vector + cloning vector - A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. - cloning vector + A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. + cloning vector @@ -24258,11 +24517,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - restriction enzyme based cloning + restriction enzyme based cloning - restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. - Kevin Clancy, Bjoern Peters - restriction enzyme based cloning + restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. + Kevin Clancy, Bjoern Peters + restriction enzyme based cloning @@ -24283,12 +24542,12 @@ the role 'adjuvant role' inheres in some 'material entity' a - Student's t-test + Student's t-test - Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. - James Malone - WEB: http://en.wikipedia.org/wiki/T-test - Student's t-test + Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. + James Malone + WEB: http://en.wikipedia.org/wiki/T-test + Student's t-test @@ -24297,12 +24556,12 @@ the role 'adjuvant role' inheres in some 'material entity' a - material sample role - a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. + material sample role + a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. - A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. - 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. - material sample role + A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. + 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. + material sample role @@ -24311,13 +24570,13 @@ the role 'adjuvant role' inheres in some 'material entity' a - topologically preserved clustered data set - the output data set generated from a self-organizing map. + topologically preserved clustered data set + the output data set generated from a self-organizing map. - A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. - James Malone - PERSON: James Malone - topologically preserved clustered data set + A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. + James Malone + PERSON: James Malone + topologically preserved clustered data set @@ -24352,11 +24611,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest + nucleic acid restriction enzyme digest - A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site - Kevin Clancy, Bjoern Peters - nucleic acid restriction enzyme digest + A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site + Kevin Clancy, Bjoern Peters + nucleic acid restriction enzyme digest @@ -24383,12 +24642,12 @@ the role 'adjuvant role' inheres in some 'material entity' a immune response assay - Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. + Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. - An assay that determines information about an immune response - Bjoern Peters - Randi Vita - IEDB + An assay that determines information about an immune response + Bjoern Peters + Randi Vita + IEDB immune response assay @@ -24413,13 +24672,13 @@ the role 'adjuvant role' inheres in some 'material entity' a - material sampling process + material sampling process - A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity + A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity sample collection sampling https://github.com/obi-ontology/obi/issues/1002 - material sampling process + material sampling process @@ -24439,14 +24698,14 @@ the role 'adjuvant role' inheres in some 'material entity' a - material sample - blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. + material sample + blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. - A material entity that has the material sample role - OBI: workshop - sample population - sample - material sample + A material entity that has the material sample role + OBI: workshop + sample population + sample + material sample @@ -24557,12 +24816,12 @@ the role 'adjuvant role' inheres in some 'material entity' a bisulfite sequencing assay - PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. + PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. - A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. - Philippe Rocca-Serra - Sagar Jain - url:https://en.wikipedia.org/wiki/Bisulfite_sequencing + A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. + Philippe Rocca-Serra + Sagar Jain + url:https://en.wikipedia.org/wiki/Bisulfite_sequencing bisulfite sequencing assay @@ -24582,7 +24841,7 @@ the role 'adjuvant role' inheres in some 'material entity' a A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone - classification and regression trees + classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART @@ -24599,20 +24858,20 @@ the role 'adjuvant role' inheres in some 'material entity' a - independent variable specification + independent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert experimental factor independent variable - Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. - study factor + Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + study factor study design independent variable @@ -24628,18 +24887,18 @@ the role 'adjuvant role' inheres in some 'material entity' a - dependent variable specification + dependent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert dependent variable - WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design dependent variable @@ -24665,12 +24924,12 @@ the role 'adjuvant role' inheres in some 'material entity' a - anticoagulant-containing test tube + anticoagulant-containing test tube - A 'blue top' test tube that contains anticoagulant for storing blood specimens' - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - anticoagulant-containing test tube + A 'blue top' test tube that contains anticoagulant for storing blood specimens' + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + anticoagulant-containing test tube @@ -24685,18 +24944,18 @@ the role 'adjuvant role' inheres in some 'material entity' a - controlled variable specification + controlled variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert controlled variable - WEB: http://en.wikipedia.org/wiki/Control_variable - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + WEB: http://en.wikipedia.org/wiki/Control_variable + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design controlled variable @@ -24768,12 +25027,12 @@ the role 'adjuvant role' inheres in some 'material entity' a human antithrombin-III in blood assay - PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. + PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. - An assay that measures the amount of antithrombin III in blood. - Alan Ruttenberg - AT-III assay - url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 + An assay that measures the amount of antithrombin III in blood. + Alan Ruttenberg + AT-III assay + url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 human antithrombin-III in blood assay @@ -24801,10 +25060,10 @@ the role 'adjuvant role' inheres in some 'material entity' a - fluorescently labeled MHC multimer + fluorescently labeled MHC multimer - A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand - fluorescently labeled MHC multimer + A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand + fluorescently labeled MHC multimer @@ -24813,13 +25072,13 @@ the role 'adjuvant role' inheres in some 'material entity' a - survival rate + survival rate - A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. - Oliver He - adapted from wikipedia + A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. + Oliver He + adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate - survival rate + survival rate @@ -24828,11 +25087,11 @@ http://en.wikipedia.org/wiki/Survival_rate - recombinant BAC cloning + recombinant BAC cloning - Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material - http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome - recombinant BAC cloning + Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material + http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome + recombinant BAC cloning @@ -24841,13 +25100,13 @@ http://en.wikipedia.org/wiki/Survival_rate - multiple testing correction objective - Application of the Bonferroni correction + multiple testing correction objective + Application of the Bonferroni correction - A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously - multiple comparison correction objective - http://en.wikipedia.org/wiki/Multiple_Testing_Correction - multiple testing correction objective + A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously + multiple comparison correction objective + http://en.wikipedia.org/wiki/Multiple_Testing_Correction + multiple testing correction objective @@ -24862,13 +25121,13 @@ http://en.wikipedia.org/wiki/Survival_rate - statistical model validation - Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia + statistical model validation + Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. - Helen Parkinson - http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 - statistical model validation + A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + Helen Parkinson + http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 + statistical model validation @@ -24899,13 +25158,13 @@ http://en.wikipedia.org/wiki/Survival_rate - double blind study execution + double blind study execution - A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#double - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - double blind study execution + A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#double + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + double blind study execution @@ -24914,11 +25173,11 @@ http://en.wikipedia.org/wiki/Survival_rate - transcription factor binding site + transcription factor binding site - SO:0000235 - PLace_holder for sequence ontology term - transcription factor binding site + SO:0000235 + PLace_holder for sequence ontology term + transcription factor binding site @@ -24933,15 +25192,15 @@ http://en.wikipedia.org/wiki/Survival_rate - glucometer - Diabetic patients use glucometers to determine their glucose levels + glucometer + Diabetic patients use glucometers to determine their glucose levels - A measurement device with the function to measure and record the level/amount of glucose in a blood sample - PERSON:Frank Gibson - PERSON:Helen Parkinson - glucose meter - http://en.wikipedia.org/wiki/Glucose_meter - glucometer + A measurement device with the function to measure and record the level/amount of glucose in a blood sample + PERSON:Frank Gibson + PERSON:Helen Parkinson + glucose meter + http://en.wikipedia.org/wiki/Glucose_meter + glucometer @@ -24950,15 +25209,15 @@ http://en.wikipedia.org/wiki/Survival_rate - purification objective - the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. + purification objective + the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. - The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest - PERSON:Bjoern Peters - isolation objective - BP - 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality - purification objective + The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest + PERSON:Bjoern Peters + isolation objective + BP + 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality + purification objective @@ -24968,10 +25227,10 @@ http://en.wikipedia.org/wiki/Survival_rate obsolete_primary structure of protein - SIINFEKL' is the primary structure of a peptide + SIINFEKL' is the primary structure of a peptide - The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together - Person:Bjoern Peters + The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together + Person:Bjoern Peters obsolete_primary structure of protein true @@ -24983,13 +25242,13 @@ http://en.wikipedia.org/wiki/Survival_rate - capsule shell + capsule shell - a small rounded gelatinous container - Person:Alan Ruttenberg - http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - capsule shell + a small rounded gelatinous container + Person:Alan Ruttenberg + http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + capsule shell @@ -24998,13 +25257,13 @@ http://en.wikipedia.org/wiki/Survival_rate - recombinant phage cloning - Insert selection by BamHI methyltransferase protection in P1 phage-based cloning + recombinant phage cloning + Insert selection by BamHI methyltransferase protection in P1 phage-based cloning - Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. - Helen Parkinson - http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 - recombinant phage cloning + Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. + Helen Parkinson + http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 + recombinant phage cloning @@ -25025,13 +25284,13 @@ http://en.wikipedia.org/wiki/Survival_rate - cross linking - cross linking can be used as a probe to link proteins together, to check protein protein interactions + cross linking + cross linking can be used as a probe to link proteins together, to check protein protein interactions - A process in which bonds are created that link one polymer to another - PERSON: Chris Stoeckert - http://en.wikipedia.org/wiki/Cross-link - cross linking + A process in which bonds are created that link one polymer to another + PERSON: Chris Stoeckert + http://en.wikipedia.org/wiki/Cross-link + cross linking @@ -25040,15 +25299,15 @@ http://en.wikipedia.org/wiki/Survival_rate - spike train datum - Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog + spike train datum + Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog - A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. - needs more work to see exactly what the data set looks like - HP - Helen Parkinson, Alan Ruttenberg - spike train measurement - Jessica Turner, NIF - spike train datum + A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. + needs more work to see exactly what the data set looks like - HP + Helen Parkinson, Alan Ruttenberg + spike train measurement + Jessica Turner, NIF + spike train datum @@ -25075,11 +25334,11 @@ http://en.wikipedia.org/wiki/Survival_rate prothrombin time assay - PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). + PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). - An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. - Alan Ruttenberg - url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 + An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. + Alan Ruttenberg + url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 prothrombin time assay @@ -25108,12 +25367,12 @@ http://en.wikipedia.org/wiki/Survival_rate - denaturing - Denaturing DNA in alcohol + denaturing + Denaturing DNA in alcohol - Is a process in which the tertiary or secondary structure of a polymer is disrupted - http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 - denaturing + Is a process in which the tertiary or secondary structure of a polymer is disrupted + http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 + denaturing @@ -25151,13 +25410,13 @@ http://en.wikipedia.org/wiki/Survival_rate - informing investigator of subject study arm + informing investigator of subject study arm - A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. - 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informing investigator of subject study arm + A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informing investigator of subject study arm @@ -25186,9 +25445,9 @@ http://en.wikipedia.org/wiki/Survival_rate antithrombin-III berichrome assay - An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard - AT-III assay - url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 + An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard + AT-III assay + url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 antithrombin-III berichrome assay @@ -25198,12 +25457,12 @@ http://en.wikipedia.org/wiki/Survival_rate - material maintenance objective + material maintenance objective - An objective specification maintains some or all of the qualities of a material over time. - PERSON: Bjoern Peters - PERSON: Bjoern Peters - material maintenance objective + An objective specification maintains some or all of the qualities of a material over time. + PERSON: Bjoern Peters + PERSON: Bjoern Peters + material maintenance objective @@ -25228,14 +25487,14 @@ http://en.wikipedia.org/wiki/Survival_rate - presentation of stimulus - The presentation of a flashing light to a monkey during reward training + presentation of stimulus + The presentation of a flashing light to a monkey during reward training - a planned process in which an organism is exposed to some stimulus with the intent to invoke an action - Helen Parkinson, Jessica Turner, Dirk Derom - stimulation of organism - Helen Parkinson, Jessica Turner, Dirk Derom - presentation of stimulus + a planned process in which an organism is exposed to some stimulus with the intent to invoke an action + Helen Parkinson, Jessica Turner, Dirk Derom + stimulation of organism + Helen Parkinson, Jessica Turner, Dirk Derom + presentation of stimulus @@ -25262,11 +25521,11 @@ http://en.wikipedia.org/wiki/Survival_rate spectrolyse heparin antifactor-Xa assay - PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). + PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). - An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. - Alan Ruttenberg - url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 + An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. + Alan Ruttenberg + url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 spectrolyse heparin antifactor-Xa assay @@ -25288,13 +25547,13 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA - Amplied DNA created by PCR + amplified DNA + Amplied DNA created by PCR - DNA that has been produced in an enzymatic amplification process - PERSON: Alan Ruttenberg - Alan Ruttenberg - amplified DNA + DNA that has been produced in an enzymatic amplification process + PERSON: Alan Ruttenberg + Alan Ruttenberg + amplified DNA @@ -25320,14 +25579,14 @@ http://en.wikipedia.org/wiki/Survival_rate - informed consent process + informed consent process - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. - 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#informed - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informed consent process + A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#informed + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informed consent process @@ -25347,12 +25606,12 @@ http://en.wikipedia.org/wiki/Survival_rate - primary structure of DNA macromolecule + primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. - placeholder for SO - BP et al - primary structure of DNA macromolecule + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + placeholder for SO + BP et al + primary structure of DNA macromolecule @@ -25362,12 +25621,12 @@ http://en.wikipedia.org/wiki/Survival_rate measuring neural activity in the caudate nucleus assay - An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus + An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus - An assay that measures neural activity in the caudate nucleus - Helen Parkinson - Dirk Derom, OBI - Jessica Turner, NIF + An assay that measures neural activity in the caudate nucleus + Helen Parkinson + Dirk Derom, OBI + Jessica Turner, NIF measuring neural activity in the caudate nucleus assay @@ -25377,14 +25636,14 @@ http://en.wikipedia.org/wiki/Survival_rate - to be treated with active ingredient role - Role of a patient in a group treated with an active substance in a clinical trial + to be treated with active ingredient role + Role of a patient in a group treated with an active substance in a clinical trial - A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient - Person:Alan Ruttenberg - PERSON: Helen Parkinson - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - to be treated with active ingredient role + A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient + Person:Alan Ruttenberg + PERSON: Helen Parkinson + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + to be treated with active ingredient role @@ -25393,12 +25652,12 @@ http://en.wikipedia.org/wiki/Survival_rate - guar gum + guar gum - Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. - Helen Parkinson - http://en.wikipedia.org/wiki/Guar_gum - guar gum + Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. + Helen Parkinson + http://en.wikipedia.org/wiki/Guar_gum + guar gum @@ -25407,13 +25666,13 @@ http://en.wikipedia.org/wiki/Survival_rate - Berichrom(r) Antithrombin III (A) Kit + Berichrom(r) Antithrombin III (A) Kit - For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution - Person:Alan Ruttenberg - WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Berichrom(r) Antithrombin III (A) Kit + For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution + Person:Alan Ruttenberg + WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Berichrom(r) Antithrombin III (A) Kit @@ -25428,14 +25687,14 @@ http://en.wikipedia.org/wiki/Survival_rate - micro electrode - A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus + micro electrode + A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus - An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. - Helen Parkinson, Jessica Turner, Dirk Derom - micro electrode measuring device - Jessica Turner, Dirk Derom - micro electrode + An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. + Helen Parkinson, Jessica Turner, Dirk Derom + micro electrode measuring device + Jessica Turner, Dirk Derom + micro electrode @@ -25444,12 +25703,12 @@ http://en.wikipedia.org/wiki/Survival_rate - fucoidan + fucoidan - Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). - Helen Parkinson - http://en.wikipedia.org/wiki/Fucoidan - fucoidan + Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). + Helen Parkinson + http://en.wikipedia.org/wiki/Fucoidan + fucoidan @@ -25470,13 +25729,13 @@ http://en.wikipedia.org/wiki/Survival_rate - calibration - the process of using pH buffer adjust a pH meter + calibration + the process of using pH buffer adjust a pH meter - A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. - GROUP: OBI Philly workshop - WEB:http://en.wikipedia.org/wiki/calibration - calibration + A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. + GROUP: OBI Philly workshop + WEB:http://en.wikipedia.org/wiki/calibration + calibration @@ -25509,12 +25768,12 @@ http://en.wikipedia.org/wiki/Survival_rate - anticoagulant tube storage of blood specimen + anticoagulant tube storage of blood specimen - Storage of a blood specimen in a tube with anticoagulant - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - anticoagulant tube storage of blood specimen + Storage of a blood specimen in a tube with anticoagulant + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + anticoagulant tube storage of blood specimen @@ -25587,14 +25846,14 @@ http://en.wikipedia.org/wiki/Survival_rate activated partial thromboplastin time assay - The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) - - An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. - There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). - Alan Ruttenberg - OBI call - aPTT assay - url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 + The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) + + An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. + There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). + Alan Ruttenberg + OBI call + aPTT assay + url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 activated partial thromboplastin time assay @@ -25610,13 +25869,13 @@ http://en.wikipedia.org/wiki/Survival_rate - filled capsule + filled capsule - A pill in the form of a small rounded gelatinous container with medicine inside. - Person:Alan Ruttenberg - http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - filled capsule + A pill in the form of a small rounded gelatinous container with medicine inside. + Person:Alan Ruttenberg + http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + filled capsule @@ -25640,13 +25899,13 @@ http://en.wikipedia.org/wiki/Survival_rate - single blind study execution + single blind study execution - A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#single - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - single blind study execution + A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#single + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + single blind study execution @@ -25673,11 +25932,11 @@ http://en.wikipedia.org/wiki/Survival_rate thrombin time assay - PMID:19696660#The thrombin time was determined using thromboclotin assay kit. + PMID:19696660#The thrombin time was determined using thromboclotin assay kit. - An assay that measures the time between the addition of the thrombin and the clot formation in plasma. - Alan Ruttenberg - url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 + An assay that measures the time between the addition of the thrombin and the clot formation in plasma. + Alan Ruttenberg + url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 thrombin time assay @@ -25687,13 +25946,13 @@ http://en.wikipedia.org/wiki/Survival_rate - recombinant YAC cloning - Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 + recombinant YAC cloning + Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 - Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material - Helen Parkinson - http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 - recombinant YAC cloning + Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material + Helen Parkinson + http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 + recombinant YAC cloning @@ -25702,12 +25961,12 @@ http://en.wikipedia.org/wiki/Survival_rate - to be treated with placebo role + to be treated with placebo role - A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - to be treated with placebo role + A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + to be treated with placebo role @@ -25722,13 +25981,13 @@ http://en.wikipedia.org/wiki/Survival_rate - treatment portion of study execution + treatment portion of study execution - A planned process, part of a study design execution, during which the treatment of subjects is ongoing - 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - treatment portion of study execution + A planned process, part of a study design execution, during which the treatment of subjects is ongoing + 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + treatment portion of study execution @@ -25737,13 +25996,13 @@ http://en.wikipedia.org/wiki/Survival_rate - pill + pill - A dose of medicine or placebo in the form of a small pellet. - Person:Alan Ruttenberg - http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - pill + A dose of medicine or placebo in the form of a small pellet. + Person:Alan Ruttenberg + http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + pill @@ -25752,12 +26011,12 @@ http://en.wikipedia.org/wiki/Survival_rate - research organization - The SALK institute is a research organization. + research organization + The SALK institute is a research organization. - An organization formed with a goal to have its members conduct investigations - Person:Bjoern Peters - research organization + An organization formed with a goal to have its members conduct investigations + Person:Bjoern Peters + research organization @@ -25768,8 +26027,8 @@ http://en.wikipedia.org/wiki/Survival_rate obsolete_primary structure of sequence macromolecule - A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds - Person:Bjoern Peters + A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds + Person:Bjoern Peters obsolete_primary structure of sequence macromolecule true @@ -25781,10 +26040,10 @@ http://en.wikipedia.org/wiki/Survival_rate - DNA residue methylation + DNA residue methylation - a quality of a DNA residue that has a methyl group attached to it - DNA residue methylation + a quality of a DNA residue that has a methyl group attached to it + DNA residue methylation @@ -25804,13 +26063,13 @@ http://en.wikipedia.org/wiki/Survival_rate - measurement device - A ruler, a microarray scanner, a Geiger counter. + measurement device + A ruler, a microarray scanner, a Geiger counter. - A device in which a measure function inheres. - GROUP:OBI Philly workshop - OBI - measurement device + A device in which a measure function inheres. + GROUP:OBI Philly workshop + OBI + measurement device @@ -25819,13 +26078,13 @@ http://en.wikipedia.org/wiki/Survival_rate - high molecular weight DNA extract - Extraction of chromosomal DNA from mammalian cells by first isolating nucei + high molecular weight DNA extract + Extraction of chromosomal DNA from mammalian cells by first isolating nucei - The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. - PERSON:Chris Stoeckert - OBI - high molecular weight DNA extract + The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. + PERSON:Chris Stoeckert + OBI + high molecular weight DNA extract @@ -25850,10 +26109,10 @@ http://en.wikipedia.org/wiki/Survival_rate - manufacturer + manufacturer - A person or organization that has a manufacturer role - manufacturer + A person or organization that has a manufacturer role + manufacturer @@ -25861,21 +26120,21 @@ http://en.wikipedia.org/wiki/Survival_rate - + - test tube + test tube - A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material - Bjoern Peters - collection tube - sample tube - http://en.wikipedia.org/wiki/Test_tube - test tube + A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material + Bjoern Peters + collection tube + sample tube + http://en.wikipedia.org/wiki/Test_tube + test tube @@ -25922,12 +26181,12 @@ http://en.wikipedia.org/wiki/Survival_rate - oral ingestion of pill + oral ingestion of pill - An adding a material entity to target with the entity is a pill and the target is the mouth - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - oral ingestion of pill + An adding a material entity to target with the entity is a pill and the target is the mouth + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + oral ingestion of pill @@ -25942,10 +26201,10 @@ http://en.wikipedia.org/wiki/Survival_rate - material maintenance + material maintenance - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time - material maintenance + a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + material maintenance @@ -25966,14 +26225,14 @@ http://en.wikipedia.org/wiki/Survival_rate - labeled oligonucleotide - + labeled oligonucleotide + - a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide - 2010-01-31: Philippe Rocca-Serra + a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide + 2010-01-31: Philippe Rocca-Serra placeholder - Person: Philippe Rocca-Serra - labeled oligonucleotide + Person: Philippe Rocca-Serra + labeled oligonucleotide @@ -25996,12 +26255,12 @@ placeholder - unblinding process + unblinding process - The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - unblinding process + The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + unblinding process @@ -26016,13 +26275,13 @@ placeholder - subject agrees they understand informed consent document + subject agrees they understand informed consent document - A process in which a subject receives an informed consent document and agrees that they have understood it - 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - subject agrees they understand informed consent document + A process in which a subject receives an informed consent document and agrees that they have understood it + 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + subject agrees they understand informed consent document @@ -26050,13 +26309,13 @@ placeholder - informing subject of study arm + informing subject of study arm - A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. - 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informing subject of study arm + A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informing subject of study arm @@ -26077,13 +26336,13 @@ placeholder - Sysmex CA-6000 Coagulation Analyzer + Sysmex CA-6000 Coagulation Analyzer - The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays - Person:Alan Ruttenberg - web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Sysmex CA-6000 Coagulation Analyzer + The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays + Person:Alan Ruttenberg + web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Sysmex CA-6000 Coagulation Analyzer @@ -26091,17 +26350,19 @@ placeholder - - hospital - human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] + + obsolete hospital + human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] - A medical organization at which sick or injured people are given clinical care - Person:Alan Ruttenberg - Person:Helen Parkinson - http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n - modified from the wording of the wordnet definition - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - hospital + A medical organization at which sick or injured people are given clinical care + Person:Alan Ruttenberg + Person:Helen Parkinson + modified from the wording of the wordnet definition; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n + + https://github.com/obi-ontology/obi/issues/1295 + + obsolete hospital + true @@ -26121,11 +26382,11 @@ placeholder - primary structure of RNA molecule + primary structure of RNA molecule - The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together - Person:Bjoern Peters - primary structure of RNA molecule + The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together + Person:Bjoern Peters + primary structure of RNA molecule @@ -26134,13 +26395,13 @@ placeholder - test substance role - fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally + test substance role + fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally - A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation - Person:Alan Ruttenberg - Group:OBI - test substance role + A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation + Person:Alan Ruttenberg + Group:OBI + test substance role @@ -26149,13 +26410,13 @@ placeholder - polyA RNA extraction + polyA RNA extraction - A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - polyA RNA extraction + A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + polyA RNA extraction @@ -26164,13 +26425,13 @@ placeholder - organellar RNA extraction + organellar RNA extraction - A RNA extraction process in which the desired output material is RNA in the organelle(s). - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - organellar RNA extraction + A RNA extraction process in which the desired output material is RNA in the organelle(s). + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + organellar RNA extraction @@ -26192,14 +26453,14 @@ placeholder - record of missing knowledge - A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. + record of missing knowledge + A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. - a information content entity created to indicate that information about something is not available to the person recording it. - This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. - Bjoern Peters - - record of missing knowledge + a information content entity created to indicate that information about something is not available to the person recording it. + This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. + Bjoern Peters + + record of missing knowledge @@ -26233,13 +26494,13 @@ placeholder western blot assay - Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. + Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. - An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. - IEDB - Philippe Rocca-Serra - IEDB - Philippe Rocca-Serra + An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. + IEDB + Philippe Rocca-Serra + IEDB + Philippe Rocca-Serra western blot assay @@ -26249,14 +26510,14 @@ placeholder - total RNA extraction + total RNA extraction - A RNA extraction process in which total cellular and organelle RNA are extracted. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - - total RNA extraction + A RNA extraction process in which total cellular and organelle RNA are extracted. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + + total RNA extraction @@ -26267,10 +26528,10 @@ placeholder obsolete intracellular material detection by flow cytometry assay - An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. + An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. - intracellular staining + intracellular staining obsolete intracellular material detection by flow cytometry assay true @@ -26287,12 +26548,12 @@ placeholder - complementary nucleotide probe role - A primer in a PCR reaction. A probe on an Affymetrix chip. + complementary nucleotide probe role + A primer in a PCR reaction. A probe on an Affymetrix chip. - A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence - PERSON:Bjoern Peters - complementary nucleotide probe role + A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence + PERSON:Bjoern Peters + complementary nucleotide probe role @@ -26307,13 +26568,13 @@ placeholder - record of unknown sex - A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. + record of unknown sex + A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. - a record indicating that the biological sex of an organism is not known. - I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. - Bjoern Peters - record of unknown sex + a record indicating that the biological sex of an organism is not known. + I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. + Bjoern Peters + record of unknown sex @@ -26322,13 +26583,13 @@ placeholder - cytoplasmic RNA extraction + cytoplasmic RNA extraction - A RNA extraction process in which the desired output material is RNA in the cytoplasm. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - cytoplasmic RNA extraction + A RNA extraction process in which the desired output material is RNA in the cytoplasm. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + cytoplasmic RNA extraction @@ -26368,12 +26629,12 @@ placeholder northern blot assay - The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. + The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. - An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. - Philippe Rocca-Serra - Richard Scheuermann - northern blot + An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. + Philippe Rocca-Serra + Richard Scheuermann + northern blot northern blot assay @@ -26383,11 +26644,11 @@ placeholder - Likelihood-ratio test + Likelihood-ratio test - Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. - Tina Boussard - Likelihood-ratio test + Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. + Tina Boussard + Likelihood-ratio test @@ -26402,14 +26663,14 @@ placeholder - nuclear RNA extract - Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) + nuclear RNA extract + Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) - A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - nuclear RNA extract + A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + nuclear RNA extract @@ -26444,10 +26705,10 @@ placeholder 96-well neutralization assay - A serum neutralization of viral infectivity assay which is performed in a 96-well plate. - Bjoern Peters - Melanie Courtot - microneutralization assay + A serum neutralization of viral infectivity assay which is performed in a 96-well plate. + Bjoern Peters + Melanie Courtot + microneutralization assay 96-well neutralization assay @@ -26463,13 +26724,13 @@ placeholder - establishing cancer cell line - Establishment of HeLa immortal cell line + establishing cancer cell line + Establishment of HeLa immortal cell line - is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal - - Helen Parkinson - establishing cancer cell line + is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal + + Helen Parkinson + establishing cancer cell line @@ -26478,12 +26739,12 @@ placeholder - pattern matching objective + pattern matching objective - A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. - Tina Boussard - http://en.wikipedia.org/wiki/Pattern_matching - pattern matching objective + A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. + Tina Boussard + http://en.wikipedia.org/wiki/Pattern_matching + pattern matching objective @@ -26498,14 +26759,14 @@ placeholder - polyA RNA extract - Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) + polyA RNA extract + Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) - A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - polyA RNA extract + A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + polyA RNA extract @@ -26532,9 +26793,9 @@ placeholder single-nucleotide-resolution nucleic acid structure mapping assay - An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. - Philippe Rocca-Serra - RNAO + An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. + Philippe Rocca-Serra + RNAO single-nucleotide-resolution nucleic acid structure mapping assay @@ -26557,16 +26818,16 @@ placeholder viral hemagglutination assay - Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. - - An assay that quantifies viruses by their hemagglutination activity. - Bjoern Peters - Melanie Courtot - Randi Vita - HA - HI - viral haemagglutinin assay - url:http://en.wikipedia.org/wiki/Hemagglutination_assay + Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. + + An assay that quantifies viruses by their hemagglutination activity. + Bjoern Peters + Melanie Courtot + Randi Vita + HA + HI + viral haemagglutinin assay + url:http://en.wikipedia.org/wiki/Hemagglutination_assay viral hemagglutination assay @@ -26647,11 +26908,11 @@ placeholder serum neutralization of viral infectivity assay - An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. - Bjoern Peters - Melanie Courtot - influenza neutralization assay - url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ + An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. + Bjoern Peters + Melanie Courtot + influenza neutralization assay + url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ serum neutralization of viral infectivity assay @@ -26688,13 +26949,13 @@ placeholder - pre-mortem specimen - material obtained through a liver biopsy from a human patient + pre-mortem specimen + material obtained through a liver biopsy from a human patient - a specimen that was taken from a live organism - Bjoern Peters + a specimen that was taken from a live organism + Bjoern Peters MO_705 premortem - pre-mortem specimen + pre-mortem specimen @@ -26775,11 +27036,11 @@ placeholder detection of specific nucleic acid polymers with complementary probes - Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. + Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. - An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. - IEDB - IEDB + An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. + IEDB + IEDB detection of specific nucleic acid polymers with complementary probes @@ -26820,18 +27081,18 @@ placeholder viral hemagglutination inhibition assay - Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. - - An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant. - Bjoern Peters - Melanie Courtot - Randi Vita - HAI - HIA - biological activity - hemagglutination inhibition - viral haemagglutinin inhibition assay - OBI branch derived + Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. + + An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant. + Bjoern Peters + Melanie Courtot + Randi Vita + HAI + HIA + biological activity + hemagglutination inhibition + viral haemagglutinin inhibition assay + OBI branch derived viral hemagglutination inhibition assay @@ -26847,14 +27108,14 @@ placeholder - cytoplasmic RNA extract - Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) + cytoplasmic RNA extract + Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) - A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - cytoplasmic RNA extract + A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + cytoplasmic RNA extract @@ -26875,16 +27136,16 @@ placeholder - cell line immortalization - Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs + cell line immortalization + Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs - an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line + an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line 4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective. - Bjoern Peters + Bjoern Peters 'establishing immortal cell line through directed genetic modification' - OBI - A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. - cell line immortalization + OBI + A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. + cell line immortalization @@ -26893,17 +27154,17 @@ placeholder - random primed DNA labeling - PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. + random primed DNA labeling + PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9. - a labeling in which random primers are used to uniformly label input DNA - need to add Klenow subunit of DNA polymerase I under material entity - Person: Bjoern Peters + a labeling in which random primers are used to uniformly label input DNA + need to add Klenow subunit of DNA polymerase I under material entity + Person: Bjoern Peters Person: Chris Stoeckert - Person: Philippe Rocca-Serra - PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. - random primed DNA labeling + Person: Philippe Rocca-Serra + PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. + random primed DNA labeling @@ -26924,13 +27185,13 @@ Person: Chris Stoeckert - RNA extract + RNA extract - an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - Group: UPenn Group - RNA extract + an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + Group: UPenn Group + RNA extract @@ -26960,11 +27221,11 @@ Person: Chris Stoeckert cell-cell killing assay - Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. + Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - A cytometry assay that monitors a cell population to track how many are killed by other cells. - IEDB - IEDB + A cytometry assay that monitors a cell population to track how many are killed by other cells. + IEDB + IEDB cell-cell killing assay @@ -27014,11 +27275,11 @@ Person: Chris Stoeckert in vivo cell killing assay - Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. + Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. - A cell killing assay that measures if and how many target cells are killed within an organism. - IEDB - IEDB + A cell killing assay that measures if and how many target cells are killed within an organism. + IEDB + IEDB in vivo cell killing assay @@ -27028,14 +27289,14 @@ Person: Chris Stoeckert - secondary structure of sequence macromolecule + secondary structure of sequence macromolecule - A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. + A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. - 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO - Person: Philippe Rocca-Serra - Wikipedia - secondary structure of sequence macromolecule + 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO + Person: Philippe Rocca-Serra + Wikipedia + secondary structure of sequence macromolecule @@ -27044,13 +27305,13 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - nuclear RNA extraction + nuclear RNA extraction - A RNA extraction process in which the desired output material is RNA in the nucleus. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - nuclear RNA extraction + A RNA extraction process in which the desired output material is RNA in the nucleus. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + nuclear RNA extraction @@ -27130,11 +27391,11 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La cell proliferation assay - Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. + Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. - A cytometry assay which measures the degreee to which input cells are replicating. - IEDB - IEDB + A cytometry assay which measures the degreee to which input cells are replicating. + IEDB + IEDB cell proliferation assay @@ -27232,13 +27493,13 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La Southern blot assay - PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. + PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. - An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. - Marcus Chibucos - Philippe Rocca-Serra - Southern blot - OBI + An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. + Marcus Chibucos + Philippe Rocca-Serra + Southern blot + OBI Southern blot assay @@ -27256,14 +27517,14 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La real time polymerase chain reaction assay - An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. - Bjoern Peters - Melanie Courtot - Q-PCR - kinetic polymerase chain reaction - qPCR - quantitative real time polymerase chain reaction - url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction + An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + Bjoern Peters + Melanie Courtot + Q-PCR + kinetic polymerase chain reaction + qPCR + quantitative real time polymerase chain reaction + url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time polymerase chain reaction assay @@ -27285,14 +27546,14 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - protein extract - PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. + protein extract + PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, - Person: Philippe Rocca-Serra - OBI & wikipedia - protein extract + a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, + Person: Philippe Rocca-Serra + OBI & wikipedia + protein extract @@ -27307,14 +27568,14 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - total RNA extract - Extraction of total RNA from cells with Qiagen mini RNeasy kit. + total RNA extract + Extraction of total RNA from cells with Qiagen mini RNeasy kit. - A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - total RNA extract + A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + total RNA extract @@ -27323,13 +27584,13 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - secondary structure of RNA molecule - PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. + secondary structure of RNA molecule + PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. - - 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO - Person: Philippe Rocca-Serra - secondary structure of RNA molecule + + 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO + Person: Philippe Rocca-Serra + secondary structure of RNA molecule @@ -27369,11 +27630,11 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. DEPC structure mapping assay - PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. + PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. - A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe - Philippe Rocca-Serra - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe + Philippe Rocca-Serra + RNA ontology DEPC structure mapping assay @@ -27389,14 +27650,14 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - organellar RNA extract - Extraction of organellar RNA from plant cells using organellar RNA binding protein. + organellar RNA extract + Extraction of organellar RNA from plant cells using organellar RNA binding protein. - A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - organellar RNA extract + A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + organellar RNA extract @@ -27431,13 +27692,13 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - post mortem specimen - the spleen taken from a dead mouse + post mortem specimen + the spleen taken from a dead mouse - a specimen that was taken from a dead organism - Bjoern Peters + a specimen that was taken from a dead organism + Bjoern Peters MO_416 postmortem - post mortem specimen + post mortem specimen @@ -27486,11 +27747,11 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. in vitro cell killing assay - Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. + Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. - IEDB - IEDB + A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. + IEDB + IEDB in vitro cell killing assay @@ -27531,11 +27792,11 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. reporter cell line analyte detection bioassay - CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. + CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. - An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. - IEDB - IEDB + An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. + IEDB + IEDB reporter cell line analyte detection bioassay @@ -27545,13 +27806,13 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - sequence feature annotation + sequence feature annotation - Information about a sequence region - Bjoern Peters - Bjoern Peters - place holder for sequence ontology term - sequence feature annotation + Information about a sequence region + Bjoern Peters + Bjoern Peters + place holder for sequence ontology term + sequence feature annotation @@ -27566,16 +27827,16 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - induced hemagglutination + induced hemagglutination - The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances - MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. + The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances + MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'. - person: Bjoern Peters - person: Melanie Courtot - hemeagglutination - WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination - induced hemagglutination + person: Bjoern Peters + person: Melanie Courtot + hemeagglutination + WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination + induced hemagglutination @@ -27590,15 +27851,15 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - supplying - Jackson Labs supplies mouse strains. + supplying + Jackson Labs supplies mouse strains. - The planned process of providing material entities + The planned process of providing material entities to be used in an investigation. - Jennifer Fostel - Jennifer Fostel - 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. - supplying + Jennifer Fostel + Jennifer Fostel + 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. + supplying @@ -27637,14 +27898,14 @@ to be used in an investigation. - labeled DNA extract + labeled DNA extract - a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. + a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call - Group: OBI group - Group: OBI group - labeled DNA extract + Group: OBI group + Group: OBI group + labeled DNA extract @@ -27659,15 +27920,15 @@ Added duirng Mar 1, 2010 dev call - cloacal specimen - type of sample used in the PCIRN influenza network + cloacal specimen + type of sample used in the PCIRN influenza network - A specimen obtained by inserting a swab deeply into the vent of the cloaca of + A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. - PERSON: Melanie Courtot - WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf - cloacal specimen + PERSON: Melanie Courtot + WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf + cloacal specimen @@ -27721,11 +27982,11 @@ stained with fecal material and is then placed in transport medium. radio immuno assay - To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. + To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. - An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. - IEDB - IEDB + An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. + IEDB + IEDB radio immuno assay @@ -27766,12 +28027,12 @@ stained with fecal material and is then placed in transport medium. real time reverse-transcription polymerase chain reaction assay - An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. - Bjoern Peters - Melanie Courtot - RRT-PCR - RT-rt PCR - qRT-PCR + An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. + Bjoern Peters + Melanie Courtot + RRT-PCR + RT-rt PCR + qRT-PCR real time reverse-transcription polymerase chain reaction assay @@ -27780,7 +28041,7 @@ stained with fecal material and is then placed in transport medium. - + @@ -27805,13 +28066,13 @@ stained with fecal material and is then placed in transport medium. - X-ray crystallography assay - Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. + X-ray crystallography 3D molecular structure determination assay + Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. - A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. - IEDB - IEDB - X-ray crystallography assay + A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. + IEDB + IEDB + X-ray crystallography 3D molecular structure determination assay @@ -27838,11 +28099,11 @@ stained with fecal material and is then placed in transport medium. promoter activity detection by reporter gene assay - A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. + A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. - An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. - IEDB - IEDB + An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. + IEDB + IEDB promoter activity detection by reporter gene assay @@ -27858,14 +28119,14 @@ stained with fecal material and is then placed in transport medium. - nasopharyngeal aspirate specimen - type of sample used in the PCIRN influenza network + nasopharyngeal aspirate specimen + type of sample used in the PCIRN influenza network - A speciemn which derives from nasopharyngeal mucosa after + A speciemn which derives from nasopharyngeal mucosa after aspiration. - PERSON: Melanie Courtot - WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf - nasopharyngeal aspirate specimen + PERSON: Melanie Courtot + WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf + nasopharyngeal aspirate specimen @@ -27914,17 +28175,17 @@ aspiration. - freezing storage - a fozen pellet used for later assay + freezing storage + a fozen pellet used for later assay - A storage process in temperature that maintenance the frozen status of the stored entities. - 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" + A storage process in temperature that maintenance the frozen status of the stored entities. + 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. - Person: Alan Ruttenberg, Mathias Brochhausen + Person: Alan Ruttenberg, Mathias Brochhausen MO_481 frozen_storage - OBI - freezing storage + OBI + freezing storage @@ -27967,11 +28228,12 @@ Updated both textual and logical definition. Both input and output material of f flow cytometry assay - Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. + Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. - A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. - IEDB - IEDB + A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. + IEDB + FACS + IEDB flow cytometry assay @@ -27993,14 +28255,14 @@ Updated both textual and logical definition. Both input and output material of f - nasal swab specimen - type of sample used in the PCIRN influenza network + nasal swab specimen + type of sample used in the PCIRN influenza network - A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of + A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. - PERSON: Melanie Courtot - WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf - nasal swab specimen + PERSON: Melanie Courtot + WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf + nasal swab specimen @@ -28023,14 +28285,14 @@ exudate and epithelial debris for microbiological or cellular examination. - Dulbecco's modified Eagle medium + Dulbecco's modified Eagle medium - A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. - Logical definition should contain all components listed in textual definition at some point. - PERSON:Bjoern Peters - D-MEM - DMEM - Dulbecco's modified Eagle medium + A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. + Logical definition should contain all components listed in textual definition at some point. + PERSON:Bjoern Peters + D-MEM + DMEM + Dulbecco's modified Eagle medium @@ -28045,15 +28307,15 @@ exudate and epithelial debris for microbiological or cellular examination. - animal euthanization - Rats were euthanized with CO2 + animal euthanization + Rats were euthanized with CO2 - A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject - Helen Parkinson and Melissa Haendel - animal sacrifice - Melissa Haendel - may later be refined with more specific list of organisms - animal euthanization + A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject + Helen Parkinson and Melissa Haendel + animal sacrifice + Melissa Haendel + may later be refined with more specific list of organisms + animal euthanization @@ -28096,12 +28358,12 @@ exudate and epithelial debris for microbiological or cellular examination. cytometric bead array assay - Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. + Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. - An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes. - IEDB - Luminex assay - IEDB + An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. + IEDB + Luminex assay + IEDB cytometric bead array assay @@ -28141,14 +28403,14 @@ exudate and epithelial debris for microbiological or cellular examination. - labeled RNA extract + labeled RNA extract - a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. + a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call - Group: OBI group - Group: OBI group - labeled RNA extract + Group: OBI group + Group: OBI group + labeled RNA extract @@ -28190,13 +28452,13 @@ Added duirng Mar 1, 2010 dev call - frozen specimen - Frozen blood plasma + frozen specimen + Frozen blood plasma - A specimen that has been frozen in order to store it. - Person:Alan Ruttenberg - MO_610 frozen_sample - frozen specimen + A specimen that has been frozen in order to store it. + Person:Alan Ruttenberg + MO_610 frozen_sample + frozen specimen @@ -28230,11 +28492,11 @@ Added duirng Mar 1, 2010 dev call surface plasmon resonance binding assay - Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. + Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. - A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. - IEDB - IEDB + A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. + IEDB + IEDB surface plasmon resonance binding assay @@ -28260,12 +28522,12 @@ Added duirng Mar 1, 2010 dev call - labeled specimen + labeled specimen - A specimen that has been modified in order to be able to detect it in future experiments - added during call 3/1/2010 - OBI group - labeled specimen + A specimen that has been modified in order to be able to detect it in future experiments + added during call 3/1/2010 + OBI group + labeled specimen @@ -28280,7 +28542,7 @@ Added duirng Mar 1, 2010 dev call - infectious agent + infectious agent is a material entity bearing the disposition to infect an organism IEDB @@ -28319,15 +28581,15 @@ Added duirng Mar 1, 2010 dev call - lyophilization storage - + lyophilization storage + - a storage process with input material entity and output freeze dried material for long time storage - PERSON: Chris Stoeckert - PERSON: Jie Zheng - - can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed - lyophilization storage + a storage process with input material entity and output freeze dried material for long time storage + PERSON: Chris Stoeckert + PERSON: Jie Zheng + + can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed + lyophilization storage @@ -28336,13 +28598,13 @@ Added duirng Mar 1, 2010 dev call - material combination function - A stirrer has a material combination function + material combination function + A stirrer has a material combination function - A material separation function is a function that decreases the resolution between two or more material entities. - Helen Parkinson - OBI - material combination function + A material separation function is a function that decreases the resolution between two or more material entities. + Helen Parkinson + OBI + material combination function @@ -28352,11 +28614,11 @@ Added duirng Mar 1, 2010 dev call obsolete_training service provider role - EBI provides training on databases and tools and has a training service provider role + EBI provides training on databases and tools and has a training service provider role - a service provider role which is realized by a servicer provider organization performing some training - PERSON:Helen Parkinson - OBI + a service provider role which is realized by a servicer provider organization performing some training + PERSON:Helen Parkinson + OBI obsolete_training service provider role true @@ -28374,13 +28636,13 @@ Added duirng Mar 1, 2010 dev call - calorimeter + calorimeter - A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. - PERSON:Bjoern Peters - calorimetry instrument? - http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm - calorimeter + A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. + PERSON:Bjoern Peters + calorimetry instrument? + http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm + calorimeter @@ -28424,12 +28686,12 @@ Added duirng Mar 1, 2010 dev call - study intervention + study intervention - the part of the execution of an intervention design study which is varied between two or more subjects in the study - PERSON: Bjoern Peters - GROUP: OBI - study intervention + the part of the execution of an intervention design study which is varied between two or more subjects in the study + PERSON: Bjoern Peters + GROUP: OBI + study intervention @@ -28449,11 +28711,11 @@ Added duirng Mar 1, 2010 dev call - material separation device - flow cytometer + material separation device + flow cytometer - A device with a separation function realized in a planed process - material separation device + A device with a separation function realized in a planed process + material separation device @@ -28468,13 +28730,13 @@ Added duirng Mar 1, 2010 dev call - positron emission tomography scanner + positron emission tomography scanner - A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. - PERSON:Bjoern Peters - PET scanner? - http://en.wikipedia.org/wiki/Positron_emission_tomography - positron emission tomography scanner + A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. + PERSON:Bjoern Peters + PET scanner? + http://en.wikipedia.org/wiki/Positron_emission_tomography + positron emission tomography scanner @@ -28528,10 +28790,10 @@ Added duirng Mar 1, 2010 dev call - intramuscular injection + intramuscular injection - is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe - intramuscular injection + is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe + intramuscular injection @@ -28546,12 +28808,12 @@ Added duirng Mar 1, 2010 dev call - micromanipulator + micromanipulator - A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. - PERSON:Bjoern Peters - http://en.wikipedia.org/wiki/Micromanipulator - micromanipulator + A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. + PERSON:Bjoern Peters + http://en.wikipedia.org/wiki/Micromanipulator + micromanipulator @@ -28561,11 +28823,11 @@ Added duirng Mar 1, 2010 dev call obsolete_material access provider role - A person or organization who provides access to a DNA sequencer. + A person or organization who provides access to a DNA sequencer. - a service provider role which is realized by a servicer provider organization performing access to some material - PERSON:Helen Parkinson - OBI + a service provider role which is realized by a servicer provider organization performing access to some material + PERSON:Helen Parkinson + OBI obsolete_material access provider role true @@ -28596,14 +28858,14 @@ Added duirng Mar 1, 2010 dev call - categorical measurement datum + categorical measurement datum - A measurement datum that is reported on a categorical scale - Bjoern Peters - nominal mesurement datum - Bjoern Peters + A measurement datum that is reported on a categorical scale + Bjoern Peters + nominal mesurement datum + Bjoern Peters - categorical measurement datum + categorical measurement datum @@ -28618,11 +28880,11 @@ Added duirng Mar 1, 2010 dev call - training process - e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility + training process + e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility - a process that achieves a training objective - training process + a process that achieves a training objective + training process @@ -28631,11 +28893,11 @@ Added duirng Mar 1, 2010 dev call - optical microscope + optical microscope - A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range - PERSON:Bjoern Peters - optical microscope + A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range + PERSON:Bjoern Peters + optical microscope @@ -28657,13 +28919,13 @@ Added duirng Mar 1, 2010 dev call - service consumer role - A biologist who uses a sequencing services fulfills the role of a service consumer + service consumer role + A biologist who uses a sequencing services fulfills the role of a service consumer - a role which inheres in a person who uses a service - Person:Helen Parkinson - OBI - service consumer role + a role which inheres in a person who uses a service + Person:Helen Parkinson + OBI + service consumer role @@ -28717,11 +28979,11 @@ Added duirng Mar 1, 2010 dev call - intradermal injection + intradermal injection - is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - intradermal injection + is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + intradermal injection @@ -28758,14 +29020,14 @@ Added duirng Mar 1, 2010 dev call - chemical cleavage - PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. + chemical cleavage + PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Biochimie. 2010 Feb 18. - chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent - PERSON:Philippe Rocca-Serra - RNA ontology group - chemical cleavage + chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent + PERSON:Philippe Rocca-Serra + RNA ontology group + chemical cleavage @@ -28792,12 +29054,12 @@ Biochimie. 2010 Feb 18. handedness assay - The Edinburgh handedness assay is a specific method of determing handedness + The Edinburgh handedness assay is a specific method of determing handedness - An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. - Helen Parkinson - handedness test - url:http://en.wikipedia.org/wiki/Handedness + An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. + Helen Parkinson + handedness test + url:http://en.wikipedia.org/wiki/Handedness handedness assay @@ -28813,12 +29075,12 @@ Biochimie. 2010 Feb 18. - vibration isolation table + vibration isolation table - A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. - PERSON:Bjoern Peters - United States Patent 6877711 - vibration isolation table + A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. + PERSON:Bjoern Peters + United States Patent 6877711 + vibration isolation table @@ -28827,10 +29089,10 @@ Biochimie. 2010 Feb 18. - sterilization function + sterilization function - a function to remove viable organisms from an input material - sterilization function + a function to remove viable organisms from an input material + sterilization function @@ -28858,12 +29120,12 @@ Biochimie. 2010 Feb 18. - service provider role - Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. + service provider role + Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. - is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person - PERSON:Helen Parkinson - service provider role + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + PERSON:Helen Parkinson + service provider role @@ -28878,12 +29140,12 @@ Biochimie. 2010 Feb 18. - oscilloscope + oscilloscope - A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). - PERSON:Bjoern Peters - http://en.wikipedia.org/wiki/Oscilloscope - oscilloscope + A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). + PERSON:Bjoern Peters + http://en.wikipedia.org/wiki/Oscilloscope + oscilloscope @@ -28892,12 +29154,12 @@ Biochimie. 2010 Feb 18. - accessed material role - the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism + accessed material role + the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism - is realized in a planned process where the bearer participates - AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it - accessed material role + is realized in a planned process where the bearer participates + AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it + accessed material role @@ -28938,14 +29200,14 @@ Biochimie. 2010 Feb 18. - paraffin specimen - liver tissue embedded in paraffin + paraffin specimen + liver tissue embedded in paraffin - a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_990 paraffin_sample - paraffin specimen + a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_990 paraffin_sample + paraffin specimen @@ -28977,13 +29239,13 @@ Biochimie. 2010 Feb 18. - compound treatment design + compound treatment design - an intervention design in which the treatment is the administration of a compound - This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. - PERSON: Bjoern Peters - MO_555 compound_treatment_design - compound treatment design + an intervention design in which the treatment is the administration of a compound + This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. + PERSON: Bjoern Peters + MO_555 compound_treatment_design + compound treatment design @@ -29019,11 +29281,11 @@ Biochimie. 2010 Feb 18. - oral administration + oral administration - An administering substance in vivo into the mouth of an organism - PERSON: Melanie Courtot - oral administration + An administering substance in vivo into the mouth of an organism + PERSON: Melanie Courtot + oral administration @@ -29041,15 +29303,15 @@ Biochimie. 2010 Feb 18. - processed specimen + processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. - A specimen that has been intentionally physically modified. - Bjoern Peters - Bjoern Peters + A specimen that has been intentionally physically modified. + Bjoern Peters + Bjoern Peters A tissue sample that has been sliced and stained for a histology study. - processed specimen + processed specimen @@ -29103,11 +29365,11 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - subcutaneous injection + subcutaneous injection - is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - subcutaneous injection + is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + subcutaneous injection @@ -29122,12 +29384,12 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - electrode puller + electrode puller - A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. - PERSON:Bjoern Peters - http://faculty.plattsburgh.edu/donald.slish/Puller1.html - electrode puller + A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. + PERSON:Bjoern Peters + http://faculty.plattsburgh.edu/donald.slish/Puller1.html + electrode puller @@ -29169,7 +29431,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. self reported handedness assessment - An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. + An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. self reported handedness assessment @@ -29196,10 +29458,10 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - vibrotome + vibrotome - A preparation device that uses a vibrating razor blade to cut through tissue. - vibrotome + A preparation device that uses a vibrating razor blade to cut through tissue. + vibrotome @@ -29208,14 +29470,14 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - reagent application function - An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. + reagent application function + An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. - A function that is realized when a reagent is automatically added to some research material. - PERSON: Nicole Vasilevsky, Matthew Brush - PERSON: Nicole Vasilevsky, Matthew Brush - 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? - reagent application function + A function that is realized when a reagent is automatically added to some research material. + PERSON: Nicole Vasilevsky, Matthew Brush + PERSON: Nicole Vasilevsky, Matthew Brush + 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? + reagent application function @@ -29224,13 +29486,13 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - addition of molecular tracer function - Immunohistochemical labeling of tissue sections by an autostainer staining system. + addition of molecular tracer function + Immunohistochemical labeling of tissue sections by an autostainer staining system. - A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. - PERSON: Nicole Vasilevsky, Matthew Brush - PERSON: Nicole Vasilevsky, Matthew Brush - addition of molecular tracer function + A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. + PERSON: Nicole Vasilevsky, Matthew Brush + PERSON: Nicole Vasilevsky, Matthew Brush + addition of molecular tracer function @@ -29239,13 +29501,13 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - training objective - A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package + training objective + A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package - An objective specification which is fulfilled by the provision of some training. - Helen Parkinson - OBI - training objective + An objective specification which is fulfilled by the provision of some training. + Helen Parkinson + OBI + training objective @@ -29254,13 +29516,13 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - categorical label - The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. + categorical label + The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. - Bjoern Peters - Bjoern Peters - categorical label + A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + Bjoern Peters + Bjoern Peters + categorical label @@ -29271,7 +29533,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. in live cell assay - An assay in which a measurement is made by observing entities located in a live cell. + An assay in which a measurement is made by observing entities located in a live cell. in live cell assay @@ -29312,14 +29574,14 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - lyophilized specimen - freezing dried DNA + lyophilized specimen + freezing dried DNA - a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_589 freeze_dried_sample - lyophilized specimen + a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_589 freeze_dried_sample + lyophilized specimen @@ -29355,11 +29617,11 @@ A blood specimen that has been centrifuged to obtain the white blood cells. in live organism assay - Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. + Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. - An assay in which a measurement is made by observing entities located in an organism. - Bjoern Peters - in vivo assay + An assay in which a measurement is made by observing entities located in an organism. + Bjoern Peters + in vivo assay in live organism assay @@ -29380,12 +29642,12 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - container + container - A device that can be used to restrict the location of material entities over time - 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) - PERSON: Bjoern Peters - container + A device that can be used to restrict the location of material entities over time + 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) + PERSON: Bjoern Peters + container @@ -29417,12 +29679,12 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: @@ -29433,10 +29695,10 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device @@ -29445,11 +29707,11 @@ In the examples above, a reagent is an operational component of a device, but th - dose specification - a protocol specifying to administer 1 ml of vaccine to a mouse + dose specification + a protocol specifying to administer 1 ml of vaccine to a mouse - a directive information entity that describes the dose that will be administered to a target - dose specification + a directive information entity that describes the dose that will be administered to a target + dose specification @@ -29470,15 +29732,15 @@ In the examples above, a reagent is an operational component of a device, but th 1 - scalar score from composite inputs + scalar score from composite inputs A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. Person: Jessica Turner - questionaire score + questionaire score Person: Jessica Turner JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? - scalar score from composite inputs + scalar score from composite inputs @@ -29488,14 +29750,14 @@ In the examples above, a reagent is an operational component of a device, but th - fresh specimen - a liver freshly removed from a rat + fresh specimen + a liver freshly removed from a rat - a specimen that is output of a specimen creation process used for an investigation without storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_730 fresh_sample - fresh specimen + a specimen that is output of a specimen creation process used for an investigation without storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_730 fresh_sample + fresh specimen @@ -29506,7 +29768,7 @@ In the examples above, a reagent is an operational component of a device, but th obsolete_electrically powered device - a processed material created to have a function and which requires electrical power to execute + a processed material created to have a function and which requires electrical power to execute obsolete_electrically powered device true @@ -29529,13 +29791,13 @@ In the examples above, a reagent is an operational component of a device, but th - sequence data - example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. + sequence data + example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. - Person:Chris Stoeckert - GROUP: OBI + Person:Chris Stoeckert + GROUP: OBI sequence data @@ -29579,11 +29841,11 @@ In the examples above, a reagent is an operational component of a device, but th cell-cell binding detection by flow cytometry assay - Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. + Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. - A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. - IEDB - IEDB + A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. + IEDB + IEDB cell-cell binding detection by flow cytometry assay @@ -29613,12 +29875,12 @@ In the examples above, a reagent is an operational component of a device, but th - handedness categorical measurement datum + handedness categorical measurement datum - A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally - PERSON:Alan Ruttenberg - PERSON:Jessica Turner - handedness categorical measurement datum + A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally + PERSON:Alan Ruttenberg + PERSON:Jessica Turner + handedness categorical measurement datum @@ -29646,15 +29908,15 @@ In the examples above, a reagent is an operational component of a device, but th - paraffin storage - + paraffin storage + - a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - need to specify paraffin or wax is one of specified input of the process - paraffin storage + a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + need to specify paraffin or wax is one of specified input of the process + paraffin storage @@ -29665,7 +29927,7 @@ In the examples above, a reagent is an operational component of a device, but th in container assay - An assay in which a measurement is made by observing entities located in a container. + An assay in which a measurement is made by observing entities located in a container. in container assay @@ -29676,10 +29938,10 @@ In the examples above, a reagent is an operational component of a device, but th obsolete_protocol service provider role - DNA sequencing of a sample by a core lab which returns data to the consumer + DNA sequencing of a sample by a core lab which returns data to the consumer - a service provider role which is realized by a servicer provider organization performing a protocol execution - PERSON:Helen Parkinson + a service provider role which is realized by a servicer provider organization performing a protocol execution + PERSON:Helen Parkinson obsolete_protocol service provider role true @@ -29712,13 +29974,13 @@ In the examples above, a reagent is an operational component of a device, but th - agar stab specimen + agar stab specimen - a specimen that is output of a process that cell culture inoculated into agar for long term storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_971 agar_stab - agar stab specimen + a specimen that is output of a process that cell culture inoculated into agar for long term storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_971 agar_stab + agar stab specimen @@ -29733,14 +29995,14 @@ In the examples above, a reagent is an operational component of a device, but th - computed tomography scanner + computed tomography scanner - An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. - PERSON:Bjoern Peters - CT scanner - X-ray computed tomography scanner - http://en.wikipedia.org/wiki/X-ray_computed_tomography - computed tomography scanner + An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. + PERSON:Bjoern Peters + CT scanner + X-ray computed tomography scanner + http://en.wikipedia.org/wiki/X-ray_computed_tomography + computed tomography scanner @@ -29779,11 +30041,11 @@ In the examples above, a reagent is an operational component of a device, but th - intranasal mucosal administration + intranasal mucosal administration - The administration of a substance into the intranasal mucosis of an organism - PERSON: Melanie Courtot - intranasal mucosal administration + The administration of a substance into the intranasal mucosis of an organism + PERSON: Melanie Courtot + intranasal mucosal administration @@ -29792,11 +30054,11 @@ In the examples above, a reagent is an operational component of a device, but th - dose - An organism has been injected 1ml of vaccine + dose + An organism has been injected 1ml of vaccine - A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. - dose + A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. + dose @@ -29837,12 +30099,12 @@ In the examples above, a reagent is an operational component of a device, but th - growth condition intervention design + growth condition intervention design - A study design in which the independent variable is the environmental condition in which the specimen is growing - PERSON: Bjoern Peters - MO_588 growth_condition_design - growth condition intervention design + A study design in which the independent variable is the environmental condition in which the specimen is growing + PERSON: Bjoern Peters + MO_588 growth_condition_design + growth condition intervention design @@ -29853,7 +30115,7 @@ In the examples above, a reagent is an operational component of a device, but th obsolete_DNA sequencing training service - A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments + A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments obsolete_DNA sequencing training service true @@ -29884,11 +30146,11 @@ In the examples above, a reagent is an operational component of a device, but th - performing a diagnosis - Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. + performing a diagnosis + Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. - The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis - performing a diagnosis + The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis + performing a diagnosis @@ -29908,11 +30170,11 @@ In the examples above, a reagent is an operational component of a device, but th - PCR instrument + PCR instrument - A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. - 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. - PCR instrument + A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. + 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. + PCR instrument @@ -29921,10 +30183,10 @@ In the examples above, a reagent is an operational component of a device, but th - electron microscope + electron microscope - A microscope that produces an image of an object by targeting it with an electron beam - electron microscope + A microscope that produces an image of an object by targeting it with an electron beam + electron microscope @@ -29945,14 +30207,14 @@ In the examples above, a reagent is an operational component of a device, but th 1 - Edinburgh score + Edinburgh score A score that measures the dominance of a person's right or left hand in everyday activities. - Person: Alan Ruttenberg - Person:Jessica Turner - PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 - WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html - Edinburgh score + Person: Alan Ruttenberg + Person:Jessica Turner + PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 + WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html + Edinburgh score @@ -29984,11 +30246,11 @@ In the examples above, a reagent is an operational component of a device, but th - DNA sequencing service + DNA sequencing service - A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. - Eagle-i will supply better English definition - DNA sequencing service + A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. + Eagle-i will supply better English definition + DNA sequencing service @@ -29997,13 +30259,13 @@ In the examples above, a reagent is an operational component of a device, but th - service provision objective - A sequencing centre has a service provision objective + service provision objective + A sequencing centre has a service provision objective - An objective which is fulfilled by the provision of some service e.g. a training service - Helen Parkinson - OBI - service provision objective + An objective which is fulfilled by the provision of some service e.g. a training service + Helen Parkinson + OBI + service provision objective @@ -30057,11 +30319,11 @@ In the examples above, a reagent is an operational component of a device, but th - intravenous injection + intravenous injection - is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - intravenous injection + is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + intravenous injection @@ -30086,13 +30348,13 @@ In the examples above, a reagent is an operational component of a device, but th - administration of material to specimen - Staining cells in a tissue slice with a dye. + administration of material to specimen + Staining cells in a tissue slice with a dye. - The directed combination of a material entity with a specimen. - Bjoern Peters - Bjoern Peters - administration of material to specimen + The directed combination of a material entity with a specimen. + Bjoern Peters + Bjoern Peters + administration of material to specimen @@ -30101,12 +30363,12 @@ In the examples above, a reagent is an operational component of a device, but th - device creation objective + device creation objective - an objective which aims to create a device with a specified function - PERSON: Helen Parkinson - OBI - device creation objective + an objective which aims to create a device with a specified function + PERSON: Helen Parkinson + OBI + device creation objective @@ -30115,13 +30377,13 @@ In the examples above, a reagent is an operational component of a device, but th - growth environment + growth environment - The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. - Right now this may be incomplete. Should also cover e.g. sound, light as well. - PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters - OBI group - growth environment + The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. + Right now this may be incomplete. Should also cover e.g. sound, light as well. + PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters + OBI group + growth environment @@ -30130,15 +30392,15 @@ In the examples above, a reagent is an operational component of a device, but th - questionnaire + questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. - Need to clarify if this is a document or a directive information entity (or what their connection is)) + Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster - questionnaire + questionnaire @@ -30194,14 +30456,14 @@ JZ: based on textual definition of edited document, it can be defined as N&S Edinburgh handedness assay - Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)" - - An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. - Alan Ruttenberg - Gully Burns (orcid:0000-0003-1493-865X) - Jessica Turner - PMID:5146491 - url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory + Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)" + + An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. + Alan Ruttenberg + Gully Burns (orcid:0000-0003-1493-865X) + Jessica Turner + PMID:5146491 + url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory Edinburgh handedness assay @@ -30217,14 +30479,14 @@ JZ: based on textual definition of edited document, it can be defined as N&S - Faraday cage + Faraday cage - A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. - PERSON:Bjoern Peters - Faraday shield - Wikipedia http://en.wikipedia.org/wiki/Faraday_cage - isolation function? HP - Faraday cage + A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. + PERSON:Bjoern Peters + Faraday shield + Wikipedia http://en.wikipedia.org/wiki/Faraday_cage + isolation function? HP + Faraday cage @@ -30245,14 +30507,14 @@ JZ: based on textual definition of edited document, it can be defined as N&S - agar stab storage + agar stab storage - a storage process with input cell culture and agar and output agar stab for long time storage - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - need to specify that agar is one of input for this process - agar stab storage + a storage process with input cell culture and agar and output agar stab for long time storage + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + need to specify that agar is one of input for this process + agar stab storage @@ -30331,12 +30593,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S RNASE CL3 structure mapping assay - PMID:16453415 + PMID:16453415 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse CL3 - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse CL3 + RNA ontology RNASE CL3 structure mapping assay @@ -30377,12 +30639,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S CMCT structure mapping assay - PMID:2422386 and PMID:2446263 + PMID:2422386 and PMID:2446263 - A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure - Philippe Rocca-Serra - single nucleotide resolution mapping assay using CMCT probe - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure + Philippe Rocca-Serra + single nucleotide resolution mapping assay using CMCT probe + RNA ontology CMCT structure mapping assay @@ -30404,13 +30666,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - image acquisition - Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel + image acquisition + Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel - A planned process that captures an image of an object. - PERSON: Jie Zheng - image acquisition - image creation + A planned process that captures an image of an object. + PERSON: Jie Zheng + image acquisition + image creation @@ -30443,12 +30705,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S MPE-Fe(II) structure mapping assay - PMID:6209709 + PMID:6209709 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Fe-MP probe - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Fe-MP probe + RNA ontology MPE-Fe(II) structure mapping assay @@ -30460,8 +30722,8 @@ JZ: based on textual definition of edited document, it can be defined as N&S obsolete_qualitative binding detection assay - A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. - PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum + A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. + PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum obsolete_qualitative binding detection assay true @@ -30494,12 +30756,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - nucleic acid extract + nucleic acid extract - An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. - PERSON: Jie Zheng - UPenn Group - nucleic acid extract + An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + PERSON: Jie Zheng + UPenn Group + nucleic acid extract @@ -30539,12 +30801,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S ENU structure mapping assay - PMID:7002606 and PMID:2446263 + PMID:7002606 and PMID:2446263 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using ENU probe - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using ENU probe + RNA ontology ENU structure mapping assay @@ -30619,12 +30881,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S RNASE V1 structure mapping assay - PMID:7031604 + PMID:7031604 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse V1 - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse V1 + RNA ontology RNASE V1 structure mapping assay @@ -30665,11 +30927,11 @@ JZ: based on textual definition of edited document, it can be defined as N&S kethoxal structure mapping assay - single nucleotide resolution mapping assay using Kethoxal probe + single nucleotide resolution mapping assay using Kethoxal probe - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe - Philippe Rocca-Serra - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe + Philippe Rocca-Serra + RNA ontology kethoxal structure mapping assay @@ -30719,10 +30981,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing - A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. - Philippe Rocca-Serra - RNAO and OBI - https://github.com/obi-ontology/obi/issues/808 + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. + Philippe Rocca-Serra + RNAO and OBI + https://github.com/obi-ontology/obi/issues/808 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing @@ -30763,12 +31025,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S DMS structure mapping assay - PMID:6159633 and PMID:2446263 + PMID:6159633 and PMID:2446263 - A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using DMS probe - RNA Ontology + A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using DMS probe + RNA Ontology DMS structure mapping assay @@ -30848,13 +31110,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S DNASE 1 structure mapping assay - PMID:3773731 + PMID:3773731 - A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure - Philippe Rocca-Serra - DNAse footprinting assay - single nucleotide resolution mapping assay using DNAse I - RNA ontology + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure + Philippe Rocca-Serra + DNAse footprinting assay + single nucleotide resolution mapping assay using DNAse I + RNA ontology DNASE 1 structure mapping assay @@ -30922,9 +31184,9 @@ JZ: based on textual definition of edited document, it can be defined as N&S single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing - A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. - Philippe Rocca-Serra - RNAO and OBI + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. + Philippe Rocca-Serra + RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing @@ -30965,12 +31227,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S Rhodium DNA structure mapping assay - PMID:2843807 + PMID:2843807 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Rhodium probe - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Rhodium probe + RNA ontology Rhodium DNA structure mapping assay @@ -31050,12 +31312,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S RNA ADA I RNA structure mapping assay - PMID:7527340 + PMID:7527340 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNA adenosine deaminase I - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNA adenosine deaminase I + RNA ontology RNA ADA I RNA structure mapping assay @@ -31096,12 +31358,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S Lead structure mapping assay - PMID:2686708 + PMID:2686708 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Lead probe - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Lead probe + RNA ontology Lead structure mapping assay @@ -31181,12 +31443,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S RNASE T2 structure mapping assay - PMID:6207483 + PMID:6207483 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse T2 - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse T2 + RNA ontology RNASE T2 structure mapping assay @@ -31198,9 +31460,9 @@ JZ: based on textual definition of edited document, it can be defined as N&S gene dosage assay - An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. - Bjoern Peters - David Osumi Sutherland + An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. + Bjoern Peters + David Osumi Sutherland gene dosage assay @@ -31234,12 +31496,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S Fe-BABE RNA structure mapping assay - PMID: 7862644 + PMID: 7862644 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Fe-BABE probe - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Fe-BABE probe + RNA ontology Fe-BABE RNA structure mapping assay @@ -31319,12 +31581,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S RNASE U2 structure mapping assay - PMID:409999 + PMID:409999 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse U2 - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse U2 + RNA ontology RNASE U2 structure mapping assay @@ -31341,13 +31603,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S binding constant determination assay - Determination of KD value for an antibody binding a protein using a BIACORE assay. + Determination of KD value for an antibody binding a protein using a BIACORE assay. - A binding assay where the specified output is a binding constant - Bjoern Peters - Jason Greenbaum - Randi Vita - IEDB + A binding assay where the specified output is a binding constant + Bjoern Peters + Jason Greenbaum + Randi Vita + IEDB binding constant determination assay @@ -31381,13 +31643,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S NMIA RNA structure mapping assay - PMID: 15796531 + PMID: 15796531 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe - Philippe Rocca-Serra - SHAPE mapping assay - single nucleotide resolution mapping assay using NMIA probe - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe + Philippe Rocca-Serra + SHAPE mapping assay + single nucleotide resolution mapping assay using NMIA probe + RNA ontology NMIA RNA structure mapping assay @@ -31421,12 +31683,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S Terbium RNA structure mapping assay - PMID:10772868 + PMID:10772868 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Terbium probe - RNA ontology + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Terbium probe + RNA ontology Terbium RNA structure mapping assay @@ -31454,13 +31716,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - feature extraction + feature extraction - A planed process with objective of obtaining quantified values from an image. - PERSON: Jie Zheng - MO_928: feature_extraction - - feature extraction + A planed process with objective of obtaining quantified values from an image. + PERSON: Jie Zheng + MO_928: feature_extraction + + feature extraction @@ -31500,14 +31762,14 @@ JZ: based on textual definition of edited document, it can be defined as N&S OH-radical structure mapping assay - PMID:2501870 - - A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe - Philippe Rocca-Serra - MOHCA assay - OH footprinting assay - single nucleotide resolution mapping assay using OH-radical probe - RNA ontology + PMID:2501870 + + A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe + Philippe Rocca-Serra + MOHCA assay + OH footprinting assay + single nucleotide resolution mapping assay using OH-radical probe + RNA ontology OH-radical structure mapping assay @@ -31587,12 +31849,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S RNASE T1 structure mapping assay - PMID:114514 + PMID:114514 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse T1 - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse T1 + RNA ontology RNASE T1 structure mapping assay @@ -31614,13 +31876,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - array image acquisition + array image acquisition - An image creation process that generate an image from the array. - PERSON: Jie Zheng - array image acquisition - MO_929: image_acquisition - array image creation + An image creation process that generate an image from the array. + PERSON: Jie Zheng + array image acquisition + MO_929: image_acquisition + array image creation @@ -31640,13 +31902,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - light emission device - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) + light emission device + A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) - A device which has a function to emit light. - Person:Helen Parkinson - OBI - light emission device + A device which has a function to emit light. + Person:Helen Parkinson + OBI + light emission device @@ -31666,15 +31928,15 @@ JZ: based on textual definition of edited document, it can be defined as N&S - perturbation device - - A homogenizer is a perturbation device. + perturbation device + + A homogenizer is a perturbation device. - A perturbation device is a device which is designed to perform a perturb function - Helen Parkinson - OBI Vancouver workshop 2010 - PERSON: Helen Parkinson - perturbation device + A perturbation device is a device which is designed to perform a perturb function + Helen Parkinson + OBI Vancouver workshop 2010 + PERSON: Helen Parkinson + perturbation device @@ -31702,13 +31964,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - environmental control device - A growth chamber is an environmental control device. + environmental control device + A growth chamber is an environmental control device. - An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. - Helen Parkinson - OBI - environmental control device + An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. + Helen Parkinson + OBI + environmental control device @@ -31787,12 +32049,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S Nuclease S1 structure mapping assay - PMID:363143 + PMID:363143 - A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Nuclease S1 - RNA ontology + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Nuclease S1 + RNA ontology Nuclease S1 structure mapping assay @@ -31802,12 +32064,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - specimen fixation function - e.g the function of a bar code reader used to read slide bar codes + specimen fixation function + e.g the function of a bar code reader used to read slide bar codes - a function that allows specific identification of individual speciment from one another. - EAGLE-I - specimen fixation function + a function that allows specific identification of individual speciment from one another. + EAGLE-I + specimen fixation function @@ -31818,8 +32080,8 @@ JZ: based on textual definition of edited document, it can be defined as N&S obsolete_specimen fixation function - A specimen fixation function is a function that holds or fastens an entity in a fixed position. - EAGLE-I + A specimen fixation function is a function that holds or fastens an entity in a fixed position. + EAGLE-I obsolete_specimen fixation function true @@ -31862,11 +32124,11 @@ JZ: based on textual definition of edited document, it can be defined as N&S Ruthenium structure mapping assay - PMID:3016894 + PMID:3016894 - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe - Philippe Rocca-Serra - RNA Ontology + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe + Philippe Rocca-Serra + RNA Ontology Ruthenium structure mapping assay @@ -31900,11 +32162,11 @@ JZ: based on textual definition of edited document, it can be defined as N&S inline probing RNA structure mapping assay - PMID:10573122 and PMID: 18369975 + PMID:10573122 and PMID: 18369975 - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity - Philippe Rocca-Serra - RNA ontology + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity + Philippe Rocca-Serra + RNA ontology inline probing RNA structure mapping assay @@ -31914,11 +32176,11 @@ JZ: based on textual definition of edited document, it can be defined as N&S - current amplification function + current amplification function - A current amplification function is an amplification function that increases the amplitude of a current. - EAGLE-I - current amplification function + A current amplification function is an amplification function that increases the amplitude of a current. + EAGLE-I + current amplification function @@ -31927,13 +32189,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - stabilization function - + stabilization function + - A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. - EAGLE-I - isolation function - stabilization function + A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. + EAGLE-I + isolation function + stabilization function @@ -31942,11 +32204,11 @@ JZ: based on textual definition of edited document, it can be defined as N&S - pump function + pump function - a transfer unction where the transfer requires work to move the entity, often against a gradient. - EAGLE-I - pump function + a transfer unction where the transfer requires work to move the entity, often against a gradient. + EAGLE-I + pump function @@ -31955,12 +32217,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - cell transfer function - A cell harvester has a cell transfer function. + cell transfer function + A cell harvester has a cell transfer function. - is a transfer function that displaces cells from one place to another - EAGLE-I - cell transfer function + is a transfer function that displaces cells from one place to another + EAGLE-I + cell transfer function @@ -31981,12 +32243,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - angiograph + angiograph - A device that records the patterns of pulse waves inside blood vessels. - PERSON: Erik Segerdell - http://medical-dictionary.thefreedictionary.com/angiograph - angiograph + A device that records the patterns of pulse waves inside blood vessels. + PERSON: Erik Segerdell + http://medical-dictionary.thefreedictionary.com/angiograph + angiograph @@ -32001,12 +32263,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - capillary blotter + capillary blotter - A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. - PERSON: Erik Segerdell - http://www.biometra.de/ - capillary blotter + A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. + PERSON: Erik Segerdell + http://www.biometra.de/ + capillary blotter @@ -32027,12 +32289,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - bioreactor + bioreactor - A device or system that supports a biologically active environment. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Bioreactor - bioreactor + A device or system that supports a biologically active environment. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Bioreactor + bioreactor @@ -32047,12 +32309,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - pH meter + pH meter - A device that is used to measure the pH (acidity or alkalinity) of a liquid. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/PH_meter - pH meter + A device that is used to measure the pH (acidity or alkalinity) of a liquid. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/PH_meter + pH meter @@ -32067,12 +32329,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - digital camera + digital camera - An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Digital_camera - digital camera + An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Digital_camera + digital camera @@ -32087,12 +32349,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - chip spotting device + chip spotting device - A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. - PERSON: Erik Segerdell - United States Patent 7416705 - chip spotting device + A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. + PERSON: Erik Segerdell + United States Patent 7416705 + chip spotting device @@ -32101,12 +32363,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - RNA extraction/purification instrument + RNA extraction/purification instrument - A device that is used to isolate and collect RNA for subsequent molecular analysis. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - RNA extraction/purification instrument + A device that is used to isolate and collect RNA for subsequent molecular analysis. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + RNA extraction/purification instrument @@ -32127,12 +32389,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - DNA extract + DNA extract - The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. - Person: Jie Zheng - Group: UPenn group - DNA extract + The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. + Person: Jie Zheng + Group: UPenn group + DNA extract @@ -32141,12 +32403,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - two-photon laser/detector + two-photon laser/detector - A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy - two-photon laser/detector + A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy + two-photon laser/detector @@ -32161,12 +32423,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - electrophoresis system + electrophoresis system - A device that moves charged particles through a medium by using an electric field induced by electrodes. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Category:Electrophoresis - electrophoresis system + A device that moves charged particles through a medium by using an electric field induced by electrodes. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Category:Electrophoresis + electrophoresis system @@ -32181,12 +32443,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - PET synthesizer + PET synthesizer - A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - PET synthesizer + A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + PET synthesizer @@ -32201,12 +32463,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - spinning-disk confocal microscope + spinning-disk confocal microscope - A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Nipkow_disk - spinning-disk confocal microscope + A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Nipkow_disk + spinning-disk confocal microscope @@ -32215,12 +32477,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - DNA synthesizer + DNA synthesizer - An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. - PERSON: Erik Segerdell - http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers - DNA synthesizer + An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. + PERSON: Erik Segerdell + http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers + DNA synthesizer @@ -32229,12 +32491,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - high performance liquid chromatography instrument + high performance liquid chromatography instrument - A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/High_performance_liquid_chromatography - high performance liquid chromatography instrument + A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/High_performance_liquid_chromatography + high performance liquid chromatography instrument @@ -32249,12 +32511,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microplate reader + microplate reader - A measurement device that detects biological, chemical or physical events of samples in microtiter plates. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Plate_reader - microplate reader + A measurement device that detects biological, chemical or physical events of samples in microtiter plates. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Plate_reader + microplate reader @@ -32263,12 +32525,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - ELISA microplate reader + ELISA microplate reader - A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - ELISA microplate reader + A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + ELISA microplate reader @@ -32283,12 +32545,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - spot cutter + spot cutter - A robotic device that is used to excise spots from gels. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - spot cutter + A robotic device that is used to excise spots from gels. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + spot cutter @@ -32309,12 +32571,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microwave synthesis system + microwave synthesis system - A device that is used to apply microwave irradiation to chemical reactions. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Microwave_chemistry - microwave synthesis system + A device that is used to apply microwave irradiation to chemical reactions. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Microwave_chemistry + microwave synthesis system @@ -32329,12 +32591,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - densitometer + densitometer - A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Densitometer - densitometer + A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Densitometer + densitometer @@ -32355,12 +32617,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - automatic staining machine + automatic staining machine - A device that is used to automatically stain tissue sections on slides or tissue specimens. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - automatic staining machine + A device that is used to automatically stain tissue sections on slides or tissue specimens. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + automatic staining machine @@ -32381,12 +32643,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - automatic tissue processor + automatic tissue processor - A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. - PERSON: Erik Segerdell - United States Patent 3762362 - automatic tissue processor + A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. + PERSON: Erik Segerdell + United States Patent 3762362 + automatic tissue processor @@ -32401,12 +32663,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - stereo microscope + stereo microscope - An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope - stereo microscope + An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope + stereo microscope @@ -32415,12 +32677,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - top loading balance + top loading balance - A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - top loading balance + A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + top loading balance @@ -32435,12 +32697,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - perfusion station + perfusion station - A device or system in which perfusion units are integrated. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - perfusion station + A device or system in which perfusion units are integrated. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + perfusion station @@ -32461,12 +32723,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - SPECT scanner + SPECT scanner - A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography - SPECT scanner + A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography + SPECT scanner @@ -32493,7 +32755,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S array manufacturer role - a manufacturer role which is played by the person or organization that manufactured the array + a manufacturer role which is played by the person or organization that manufactured the array PERSON: Chris Stoeckert, Jie Zheng MO_695 array_manufacturer array manufacturer role @@ -32511,12 +32773,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - scintillation counter + scintillation counter - A device that is used to measure ionizing radiation. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Scintillation_counter - scintillation counter + A device that is used to measure ionizing radiation. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Scintillation_counter + scintillation counter @@ -32531,12 +32793,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - programmable array microscope + programmable array microscope - A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. - PERSON: Erik Segerdell - Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 - programmable array microscope + A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. + PERSON: Erik Segerdell + Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 + programmable array microscope @@ -32564,12 +32826,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - cryostat + cryostat - A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cryostat - cryostat + A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Cryostat + cryostat @@ -32584,12 +32846,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microtome knife maker + microtome knife maker - A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - microtome knife maker + A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + microtome knife maker @@ -32604,12 +32866,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - cryofixation device + cryofixation device - A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cryofixation - cryofixation device + A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Cryofixation + cryofixation device @@ -32631,12 +32893,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - hybridization oven + hybridization oven - A device that creates an appropriate environment for nucleic acid hybridization. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - hybridization oven + A device that creates an appropriate environment for nucleic acid hybridization. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + hybridization oven @@ -32663,12 +32925,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - incubator shaker + incubator shaker - An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - incubator shaker + An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + incubator shaker @@ -32689,12 +32951,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - small-animal image acquisition device + small-animal image acquisition device - A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - small-animal image acquisition device + A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + small-animal image acquisition device @@ -32715,12 +32977,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - infrared image acquisition device + infrared image acquisition device - An image acquisition device that is responsive to an infrared emissive target within a given field of view. - PERSON: Erik Segerdell - United States Patent 4107530 - infrared image acquisition device + An image acquisition device that is responsive to an infrared emissive target within a given field of view. + PERSON: Erik Segerdell + United States Patent 4107530 + infrared image acquisition device @@ -32735,12 +32997,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - confocal microscope + confocal microscope - A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Confocal_microscopy - confocal microscope + A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Confocal_microscopy + confocal microscope @@ -32755,12 +33017,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - patch clamp device + patch clamp device - A device used in electrophysiology that allows the study of single or multiple ion channels in cells. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Patch_clamp - patch clamp device + A device used in electrophysiology that allows the study of single or multiple ion channels in cells. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Patch_clamp + patch clamp device @@ -32781,12 +33043,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - gel imaging system + gel imaging system - A device that is used to acquire images of laboratory gels. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - gel imaging system + A device that is used to acquire images of laboratory gels. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + gel imaging system @@ -32801,12 +33063,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - protein separation apparatus + protein separation apparatus - A device that is used for the separation of proteins. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - protein separation apparatus + A device that is used for the separation of proteins. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + protein separation apparatus @@ -32815,12 +33077,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - multichannel electronic pipette + multichannel electronic pipette - A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. - PERSON: Erik Segerdell - http://www.faqs.org/patents/app/20090196797 - multichannel electronic pipette + A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. + PERSON: Erik Segerdell + http://www.faqs.org/patents/app/20090196797 + multichannel electronic pipette @@ -32835,12 +33097,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - vitrification apparatus + vitrification apparatus - A device that is used to effect the transition of a substance into a glass. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Glass_transition - vitrification apparatus + A device that is used to effect the transition of a substance into a glass. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Glass_transition + vitrification apparatus @@ -32861,12 +33123,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - radiography instrument + radiography instrument - An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Medical_radiography - radiography instrument + An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Medical_radiography + radiography instrument @@ -32887,12 +33149,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - radiation measurement device + radiation measurement device - A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - radiation measurement device + A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + radiation measurement device @@ -32913,12 +33175,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - lyophilizer + lyophilizer - A device that is used to freeze dry material. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Freeze_drying - lyophilizer + A device that is used to freeze dry material. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Freeze_drying + lyophilizer @@ -32927,12 +33189,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - tandem mass spectrometer + tandem mass spectrometer - A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. - PERSON: Erik Segerdell - http://goldbook.iupac.org/T06250.html - tandem mass spectrometer + A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. + PERSON: Erik Segerdell + http://goldbook.iupac.org/T06250.html + tandem mass spectrometer @@ -32947,12 +33209,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microhardness tester + microhardness tester - A hardness testing device that is used in light-optical microscopes. - PERSON: Erik Segerdell - United States Patent 4611487 - microhardness tester + A hardness testing device that is used in light-optical microscopes. + PERSON: Erik Segerdell + United States Patent 4611487 + microhardness tester @@ -32961,12 +33223,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - multimode microplate reader + multimode microplate reader - A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - multimode microplate reader + A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + multimode microplate reader @@ -32975,12 +33237,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - mechanical balance + mechanical balance - A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). - PERSON: Erik Segerdell - http://www.britannica.com/EBchecked/topic/49765/balance - mechanical balance + A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). + PERSON: Erik Segerdell + http://www.britannica.com/EBchecked/topic/49765/balance + mechanical balance @@ -32989,12 +33251,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - computer cluster + computer cluster - A group of linked computers, working together closely so that in many respects they form a single computer. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cluster_(computing) - computer cluster + A group of linked computers, working together closely so that in many respects they form a single computer. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Cluster_(computing) + computer cluster @@ -33009,12 +33271,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microtome knife sharpener + microtome knife sharpener - A device that is used to sharpen knives used in microtomy. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - microtome knife sharpener + A device that is used to sharpen knives used in microtomy. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + microtome knife sharpener @@ -33029,12 +33291,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - plate shaker + plate shaker - A device that provides shaking motion for microplates. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - plate shaker + A device that provides shaking motion for microplates. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + plate shaker @@ -33049,12 +33311,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - coagulation analyzer + coagulation analyzer - A device for automatically analyzing blood coagulation in a clinical laboratory. - PERSON: Erik Segerdell - United States Patent 5439646 - coagulation analyzer + A device for automatically analyzing blood coagulation in a clinical laboratory. + PERSON: Erik Segerdell + United States Patent 5439646 + coagulation analyzer @@ -33069,12 +33331,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - laser capture microdissection microscope + laser capture microdissection microscope - A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. - PERSON: Erik Segerdell - http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine - laser capture microdissection microscope + A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. + PERSON: Erik Segerdell + http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine + laser capture microdissection microscope @@ -33089,12 +33351,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - liquid extraction robot + liquid extraction robot - A liquid handling device that provides automatic liquid extraction. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - liquid extraction robot + A liquid handling device that provides automatic liquid extraction. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + liquid extraction robot @@ -33115,12 +33377,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - ultrasound machine + ultrasound machine - A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Sonography - ultrasound machine + A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Sonography + ultrasound machine @@ -33141,12 +33403,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - immunoblot scanner + immunoblot scanner - A device that is used for the imaging of immunoblots. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - immunoblot scanner + A device that is used for the imaging of immunoblots. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + immunoblot scanner @@ -33155,12 +33417,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microcentrifuge + microcentrifuge - A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Laboratory_centrifuge - microcentrifuge + A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Laboratory_centrifuge + microcentrifuge @@ -33169,12 +33431,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - electronic repeater pipette + electronic repeater pipette - A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. - PERSON: Erik Segerdell - http://www.faqs.org/patents/app/20090196797 - electronic repeater pipette + A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. + PERSON: Erik Segerdell + http://www.faqs.org/patents/app/20090196797 + electronic repeater pipette @@ -33183,12 +33445,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - electron paramagnetic resonance spectrometer + electron paramagnetic resonance spectrometer - An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance - electron paramagnetic resonance spectrometer + An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance + electron paramagnetic resonance spectrometer @@ -33203,12 +33465,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - rocker + rocker - A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - rocker + A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + rocker @@ -33217,12 +33479,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - analytical balance + analytical balance - A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Weighing_scale - analytical balance + A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Weighing_scale + analytical balance @@ -33237,12 +33499,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - scanning force microscope + scanning force microscope - A microscope that forms images of surfaces using a physical probe that scans the specimen. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Scanning_probe_microscopy - scanning force microscope + A microscope that forms images of surfaces using a physical probe that scans the specimen. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Scanning_probe_microscopy + scanning force microscope @@ -33251,12 +33513,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - pulsed-field gel electrophoresis system + pulsed-field gel electrophoresis system - A gel electrophoresis system that is used to separate very large molecules of DNA. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis - pulsed-field gel electrophoresis system + A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis + pulsed-field gel electrophoresis system @@ -33271,12 +33533,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - tissue embedding station + tissue embedding station - A device that is used to perform paraffin embedding of tissue specimens. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - tissue embedding station + A device that is used to perform paraffin embedding of tissue specimens. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + tissue embedding station @@ -33291,12 +33553,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - nucleic acid sequencer + nucleic acid sequencer - An device that is used to determine the order of nucleotides in nucleic acid sequences. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - nucleic acid sequencer + An device that is used to determine the order of nucleotides in nucleic acid sequences. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + nucleic acid sequencer @@ -33317,12 +33579,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - bead array reader + bead array reader - A device that is used to acquire and image bead array data. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - bead array reader + A device that is used to acquire and image bead array data. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + bead array reader @@ -33331,12 +33593,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - real-time PCR machine + real-time PCR machine - An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction - real-time PCR machine + An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction + real-time PCR machine @@ -33364,12 +33626,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - paraffin oven + paraffin oven - A device that is used for the warming of paraffin embedding medium. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - paraffin oven + A device that is used for the warming of paraffin embedding medium. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + paraffin oven @@ -33396,12 +33658,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - autoclave + autoclave - A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. - PERSON: Erik Segerdell - J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave - autoclave + A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. + PERSON: Erik Segerdell + J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave + autoclave @@ -33416,12 +33678,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microplate washer + microplate washer - A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? - PERSON: Erik Segerdell - http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 - microplate washer + A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? + PERSON: Erik Segerdell + http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 + microplate washer @@ -33436,12 +33698,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - nucleic acid extraction/purification instrument + nucleic acid extraction/purification instrument - A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - nucleic acid extraction/purification instrument + A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + nucleic acid extraction/purification instrument @@ -33450,12 +33712,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - ELISA microplate washer + ELISA microplate washer - A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - ELISA microplate washer + A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + ELISA microplate washer @@ -33470,12 +33732,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - vacuum manifold + vacuum manifold - A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - vacuum manifold + A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + vacuum manifold @@ -33484,12 +33746,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - DNA extraction/purification instrument + DNA extraction/purification instrument - A device that is used to isolate and collect DNA for subsequent molecular analysis. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/DNA_extraction - DNA extraction/purification instrument + A device that is used to isolate and collect DNA for subsequent molecular analysis. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/DNA_extraction + DNA extraction/purification instrument @@ -33510,12 +33772,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - multichannel pipette + multichannel pipette - A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - multichannel pipette + A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + multichannel pipette @@ -33530,12 +33792,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - cell harvester + cell harvester - A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? - PERSON: Erik Segerdell - PERSON: Erik Segerdell - cell harvester + A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? + PERSON: Erik Segerdell + PERSON: Erik Segerdell + cell harvester @@ -33544,12 +33806,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - portable fluorometer + portable fluorometer - A compact fluorometer that can be carried or moved with ease. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - portable fluorometer + A compact fluorometer that can be carried or moved with ease. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + portable fluorometer @@ -33558,13 +33820,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - gel electrophoresis system + gel electrophoresis system - A device that moves charged particles through a medium by using an electric field induced by electrodes. - PERSON: Erik Segerdell - electrophoresis system - http://en.wikipedia.org/wiki/Category:Electrophoresis - gel electrophoresis system + An electrophoresis system in which an electric field is applied to a gel matrix + PERSON: Erik Segerdell + https://en.wikipedia.org/wiki/Gel_electrophoresis + gel electrophoresis system @@ -33579,12 +33840,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - diffractometer + diffractometer - A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Diffractometer - diffractometer + A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Diffractometer + diffractometer @@ -33599,12 +33860,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microdissection instrument + microdissection instrument - A device that is used for the dissection of tissues under magnification. - PERSON: Erik Segerdell - http://medical-dictionary.thefreedictionary.com/microdissection - microdissection instrument + A device that is used for the dissection of tissues under magnification. + PERSON: Erik Segerdell + http://medical-dictionary.thefreedictionary.com/microdissection + microdissection instrument @@ -33619,12 +33880,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - micropipette puller + micropipette puller - A device that is used to fabricate glass micropipettes. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Micropipette - micropipette puller + A device that is used to fabricate glass micropipettes. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Micropipette + micropipette puller @@ -33639,12 +33900,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - laser scanning confocal microscope + laser scanning confocal microscope - A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy - laser scanning confocal microscope + A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy + laser scanning confocal microscope @@ -33659,12 +33920,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - digital microscope + digital microscope - A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Digital_microscope - digital microscope + A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Digital_microscope + digital microscope @@ -33685,12 +33946,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - freeze substitution system + freeze substitution system - A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. - PERSON: Erik Segerdell - doi:10.1017/S143192760707866X - freeze substitution system + A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. + PERSON: Erik Segerdell + doi:10.1017/S143192760707866X + freeze substitution system @@ -33711,12 +33972,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - micropipette + micropipette - A microinjection device that is used to measure very small volumes of liquids. - PERSON: Erik Segerdell - http://www.answers.com/topic/micropipette - micropipette + A microinjection device that is used to measure very small volumes of liquids. + PERSON: Erik Segerdell + http://www.answers.com/topic/micropipette + micropipette @@ -33731,12 +33992,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - voltage clamp device + voltage clamp device - A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Voltage_clamp - voltage clamp device + A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Voltage_clamp + voltage clamp device @@ -33764,12 +34025,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - vacuum oven + vacuum oven - A device that heats materials in a vacuum. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - vacuum oven + A device that heats materials in a vacuum. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + vacuum oven @@ -33784,12 +34045,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - slide warmer + slide warmer - A device that is used to heat microscope slides. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - slide warmer + A device that is used to heat microscope slides. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + slide warmer @@ -33798,12 +34059,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - capillary electrophoresis instrument + capillary electrophoresis instrument - An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Capillary_electrophoresis - capillary electrophoresis instrument + An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Capillary_electrophoresis + capillary electrophoresis instrument @@ -33818,12 +34079,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - denaturing high-performance liquid chromatography instrument + denaturing high-performance liquid chromatography instrument - A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. - PERSON: Erik Segerdell - doi:10.1385/1-59259-850-1:173 - denaturing high-performance liquid chromatography instrument + A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. + PERSON: Erik Segerdell + doi:10.1385/1-59259-850-1:173 + denaturing high-performance liquid chromatography instrument @@ -33831,13 +34092,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - agarose gel electrophoresis system + + agarose gel electrophoresis system - A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis - agarose gel electrophoresis system + A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis + agarose gel electrophoresis system @@ -33858,12 +34119,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - balance + balance - A measuring instrument that is used to determine the weight or mass of an object. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Weighing_scale - balance + A measuring instrument that is used to determine the weight or mass of an object. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Weighing_scale + balance @@ -33878,12 +34139,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - surface plasmon resonance instrument + surface plasmon resonance instrument - A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Surface_plasmon_resonance - surface plasmon resonance instrument + A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Surface_plasmon_resonance + surface plasmon resonance instrument @@ -33898,12 +34159,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - protein sequencer + protein sequencer - An device that is used to determine the order of amino acids in protein sequences. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - protein sequencer + An device that is used to determine the order of amino acids in protein sequences. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + protein sequencer @@ -33918,13 +34179,13 @@ JZ: based on textual definition of edited document, it can be defined as N&S - X-ray source + X-ray source - A device that is used to generate X-rays. - PERSON: Erik Segerdell - x-ray generator - http://en.wikipedia.org/wiki/X-ray_generator - X-ray source + A device that is used to generate X-rays. + PERSON: Erik Segerdell + x-ray generator + http://en.wikipedia.org/wiki/X-ray_generator + X-ray source @@ -33933,12 +34194,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - liquid chromatography instrument + liquid chromatography instrument - A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated - PERSON: Matthew Brush - PERSON: Matthew Brush - liquid chromatography instrument + A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated + PERSON: Matthew Brush + PERSON: Matthew Brush + liquid chromatography instrument @@ -33970,7 +34231,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S individual organism identifier a CRID symbol used to distinguish one individual organism from another. - PERSON: Chris Stoeckert, Jie Zheng + PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier @@ -34031,14 +34292,14 @@ JZ: based on textual definition of edited document, it can be defined as N&S - labeled nucleic acid extract + labeled nucleic acid extract - a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. - Person: Jie Zheng - labeled extract - MO_221 labeledExtract - labeled extract - labeled nucleic acid extract + a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. + Person: Jie Zheng + labeled extract + MO_221 labeledExtract + labeled extract + labeled nucleic acid extract @@ -34046,25 +34307,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - - - - - - - - - - - - - + binding constant The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". - A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process - 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. + A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed. + 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant @@ -34077,27 +34325,31 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + + + + + - + - - 3D structure determination of bound complex assay - Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. + + 3D structure determination of bound molecular complex assay + Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. - A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration. - IEDB - IEDB - 3D structure determination of bound complex assay + A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. + IEDB + IEDB + 3D structure determination of bound molecular complex assay @@ -34124,12 +34376,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S binding assay - Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. + Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. - An assay with the objective to characterize the disposition of two or more material entities to form a complex. - Bjoern Peters - Jason Greenbaum - Randi Vita + An assay with the objective to characterize the disposition of two or more material entities to form a complex. + Bjoern Peters + Jason Greenbaum + Randi Vita binding assay @@ -34196,7 +34448,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' gene knock in a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. - PERSON: Chris Stoeckert, Jie Zheng + PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/Gene_Knock-in gene knock in @@ -34280,11 +34532,11 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - transfection + transfection a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell PERSON: Chris Stoeckert, Jie Zheng - MO_366 transfection + MO_366 transfection transfection @@ -34299,7 +34551,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng - suggested to be added by BP and AR during Oct 25, 2010 dev call + suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective @@ -34324,12 +34576,12 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - 3D structural organization datum - The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. + 3D structural organization datum + The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. - A measurement datum that describes the structural orientation of a material entity in 3D space. - PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters - 3D structural organization datum + A measurement datum that describes the structural orientation of a material entity in 3D space. + PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters + 3D structural organization datum @@ -34340,10 +34592,10 @@ Has term 'cell co-culturing' and 'maintaining cell culture' age since planting measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. - PERSON:Chris Stoeckert, Jie Zheng - MO_495 planting - Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. + An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. + PERSON:Chris Stoeckert, Jie Zheng + MO_495 planting + Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call age since planting measurement datum @@ -34357,9 +34609,9 @@ Supported by Alan on Nov 15, 2010 dev call age since hatching measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. - PERSON:Chris Stoeckert, Jie Zheng - MO_745 hatching + An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. + PERSON:Chris Stoeckert, Jie Zheng + MO_745 hatching age since hatching measurement datum @@ -34411,11 +34663,11 @@ Supported by Alan on Nov 15, 2010 dev call age determination assay - An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). - This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. - Alan Ruttenberg - age measurement assay - OBI group + An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). + This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. + Alan Ruttenberg + age measurement assay + OBI group age determination assay @@ -34427,9 +34679,9 @@ Supported by Alan on Nov 15, 2010 dev call age since egg laying measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. - PERSON:Chris Stoeckert, Jie Zheng - MO_767 egg laying + An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. + PERSON:Chris Stoeckert, Jie Zheng + MO_767 egg laying age since egg laying measurement datum @@ -34455,10 +34707,10 @@ Supported by Alan on Nov 15, 2010 dev call age since germination measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. - Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. - PERSON:Chris Stoeckert, Jie Zheng - MO_590 germination + An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. + Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. + PERSON:Chris Stoeckert, Jie Zheng + MO_590 germination age since germination measurement datum @@ -34468,12 +34720,12 @@ Supported by Alan on Nov 15, 2010 dev call - validation by reverse transcription PCR design + validation by reverse transcription PCR design - a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results - PERSON: Chris Stoeckert, Jie Zheng - MO_986 reverse_transcription_PCR_quality_control - validation by reverse transcription PCR design + a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results + PERSON: Chris Stoeckert, Jie Zheng + MO_986 reverse_transcription_PCR_quality_control + validation by reverse transcription PCR design @@ -34484,9 +34736,9 @@ Supported by Alan on Nov 15, 2010 dev call age since eclosion measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. - PERSON:Chris Stoeckert, Jie Zheng - MO_876 eclosion + An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. + PERSON:Chris Stoeckert, Jie Zheng + MO_876 eclosion age since eclosion measurement datum @@ -34498,9 +34750,9 @@ Supported by Alan on Nov 15, 2010 dev call age since sowing measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. - PERSON:Chris Stoeckert, Jie Zheng - MO_748 sowing + An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. + PERSON:Chris Stoeckert, Jie Zheng + MO_748 sowing age since sowing measurement datum @@ -34512,9 +34764,9 @@ Supported by Alan on Nov 15, 2010 dev call age since coitus measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. - PERSON:Chris Stoeckert, Jie Zheng - MO_783 coitus + An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. + PERSON:Chris Stoeckert, Jie Zheng + MO_783 coitus age since coitus measurement datum @@ -34524,12 +34776,12 @@ Supported by Alan on Nov 15, 2010 dev call - validation by real time PCR design + validation by real time PCR design - a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results - PERSON: Chris Stoeckert, Jie Zheng - MO_434 real_time_PCR_quality_control - validation by real time PCR design + a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results + PERSON: Chris Stoeckert, Jie Zheng + MO_434 real_time_PCR_quality_control + validation by real time PCR design @@ -34546,18 +34798,18 @@ Supported by Alan on Nov 15, 2010 dev call age measurement datum - A time measurement datum that is the result of measurement of age of an organism - note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. + A time measurement datum that is the result of measurement of age of an organism + note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage - PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng - MO_178 Age - In MageTab file, we use + PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng + MO_178 Age + In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class - discussed on Nov 15, dev call + discussed on Nov 15, dev call All subtype will be defined by textual definition now. age measurement datum @@ -34570,10 +34822,10 @@ All subtype will be defined by textual definition now. age since fertilization measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. - Definition of fertilization comes from GO. - PERSON:Chris Stoeckert, Jie Zheng - MO_701 fertilization + An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. + Definition of fertilization comes from GO. + PERSON:Chris Stoeckert, Jie Zheng + MO_701 fertilization age since fertilization measurement datum @@ -34585,9 +34837,9 @@ All subtype will be defined by textual definition now. age since birth measurement datum - An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. - PERSON:Chris Stoeckert, Jie Zheng - MO_710 birth + An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. + PERSON:Chris Stoeckert, Jie Zheng + MO_710 birth age since birth measurement datum @@ -34662,10 +34914,10 @@ All subtype will be defined by textual definition now. reverse transcription polymerase chain reaction assay - An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. - Chris Stoeckert - Jie Zheng - Penn Group + An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. + Chris Stoeckert + Jie Zheng + Penn Group reverse transcription polymerase chain reaction assay @@ -34681,13 +34933,13 @@ All subtype will be defined by textual definition now. - half life datum (t 1/2) + half life datum (t 1/2) - The time it takes for 50% of a class of stochastic processes to occur. - Bjoern Peters - t 1/2 - Bjoern Peters - half life datum (t 1/2) + The time it takes for 50% of a class of stochastic processes to occur. + Bjoern Peters + t 1/2 + Bjoern Peters + half life datum (t 1/2) @@ -34696,11 +34948,11 @@ All subtype will be defined by textual definition now. - dose response curve + dose response curve - A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. - Bjoern Peters; Randi Vita - dose response curve + A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. + Bjoern Peters; Randi Vita + dose response curve @@ -34734,13 +34986,13 @@ All subtype will be defined by textual definition now. - service - providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony + service + providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony - A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. - Carlo; Matt - OBI workshop San Diego 2011 - service + A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. + Carlo; Matt + OBI workshop San Diego 2011 + service @@ -34765,14 +35017,14 @@ All subtype will be defined by textual definition now. - passive immunization - Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. + passive immunization + Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. - The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. - PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum - adoptive transfer - passive immunization + The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. + PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum + adoptive transfer + passive immunization @@ -34783,9 +35035,9 @@ Transferring epitope specific T cells from one mouse into another. selective organism creation objective - an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. - PERSON: Chris Stoeckert, Jie Zheng - WEB: wikipedia + an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. + PERSON: Chris Stoeckert, Jie Zheng + WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 @@ -34798,13 +35050,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - Individual epitope immunization in vivo - Injection of a peptide T cell epitope into a mouse + Individual epitope immunization in vivo + Injection of a peptide T cell epitope into a mouse - An immunization in which an individual epitope is administered into a host organism. - 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here. - PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita - Individual epitope immunization in vivo + An immunization in which an individual epitope is administered into a host organism. + 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here. + PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita + Individual epitope immunization in vivo @@ -34897,9 +35149,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 RNA sequencing assay - An assay that determines the sequence of an RNA molecule. - Bjoern Peters - Bjoern Peters + An assay that determines the sequence of an RNA molecule. + Bjoern Peters + Bjoern Peters RNA sequencing assay @@ -34933,9 +35185,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 efficacy of epitope intervention experiment - An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. - Bjoern Peters - efficacy of in vivo intervention + An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. + Bjoern Peters + efficacy of in vivo intervention efficacy of epitope intervention experiment @@ -34947,9 +35199,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope protection from infectious challenge experiment - An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. - Bjoern Peters - protection from infectious challenge + An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. + Bjoern Peters + protection from infectious challenge epitope protection from infectious challenge experiment @@ -34971,14 +35223,14 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - half maximal effective concentration (EC50) - Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. + half maximal effective concentration (EC50) + Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. - half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. + half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. - Bjoern Peters; Randi Vita - wikipedia - half maximal effective concentration (EC50) + Bjoern Peters; Randi Vita + wikipedia + half maximal effective concentration (EC50) @@ -34998,11 +35250,11 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - binding datum + binding datum - A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. - Bjoern Peters; Randi Vita - binding datum + A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. + Bjoern Peters; Randi Vita + binding datum @@ -35010,11 +35262,11 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - negative binding datum + + negative binding datum - A binding datum that states that there is no significant disposition of two or more entities to form a complex - negative binding datum + A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. + negative binding datum @@ -35025,9 +35277,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope protection from tumor challenge experiment - An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. - Bjoern Peters - tumor burden after challenge + An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. + Bjoern Peters + tumor burden after challenge epitope protection from tumor challenge experiment @@ -35039,9 +35291,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope protection experiment - An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. - Bjoern Peters - protection from challenge + An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. + Bjoern Peters + protection from challenge epitope protection experiment @@ -35074,12 +35326,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 selectively maintained organism - An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms - Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert - cultivar - ecotype - strain - MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar + An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms + Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert + cultivar + ecotype + strain + MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar selectively maintained organism @@ -35091,9 +35343,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope protection from infectious challenge experiment based on pathogen burden - An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. - Bjoern Peters - pathogen urden after infectious challenge + An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. + Bjoern Peters + pathogen urden after infectious challenge epitope protection from infectious challenge experiment based on pathogen burden @@ -35115,13 +35367,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 infectious agent detection assay - Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus. + Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus. - An assay that measures the presence or amount of an infectious agent in an evaluant - Bjoern Peters - Jason Greenbaum - Randi Vita - Richard Scheuermann + An assay that measures the presence or amount of an infectious agent in an evaluant + Bjoern Peters + Jason Greenbaum + Randi Vita + Richard Scheuermann infectious agent detection assay @@ -35133,9 +35385,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope disease exacerbation experiment - An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. - Bjoern Peters - exacerbation assay + An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. + Bjoern Peters + exacerbation assay epitope disease exacerbation experiment @@ -35147,9 +35399,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope protection experiment based on survival - An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. - Bjoern Peters - host survival after challenge + An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. + Bjoern Peters + host survival after challenge epitope protection experiment based on survival @@ -35161,9 +35413,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope treatment experiment - An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. - Bjoern Peters - decreased disease symptoms after treatment + An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. + Bjoern Peters + decreased disease symptoms after treatment epitope treatment experiment @@ -35185,13 +35437,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - half maximal inhibitory concentration (IC50) - Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. + half maximal inhibitory concentration (IC50) + Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. - Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. - Bjoern Peters; Randi Vita - wikipedia - half maximal inhibitory concentration (IC50) + Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. + Bjoern Peters; Randi Vita + wikipedia + half maximal inhibitory concentration (IC50) @@ -35208,11 +35460,11 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific immune intervention + epitope specific immune intervention - An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope - Person: Bjoern Peters, Randi Vita, Jason Greenbaum - epitope specific immune intervention + An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope + Person: Bjoern Peters, Randi Vita, Jason Greenbaum + epitope specific immune intervention @@ -35232,13 +35484,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific cytokine production by T cells + epitope specific cytokine production by T cells - A process of cytokine production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific cytokine production by T cells + A process of cytokine production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific cytokine production by T cells @@ -35249,21 +35501,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells - An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|ELISPOT + An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|ELISPOT ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells @@ -35299,12 +35567,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - operator variation design + operator variation design - A study design that assesses the operator performance and relation to data consistency and quality. - Person: Chris Stoeckert, Jie Zheng - MO_519 operator_variation_design - operator variation design + A study design that assesses the operator performance and relation to data consistency and quality. + Person: Chris Stoeckert, Jie Zheng + MO_519 operator_variation_design + operator variation design @@ -35315,21 +35583,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific IP-10 production by T cells - An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|cytometric bead array + A cytometric bead array assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|cytometric bead array cytometric bead array assay measuring epitope specific IP-10 production by T cells @@ -35345,12 +35629,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - comparative genome hybridization by array design + comparative genome hybridization by array design - A study design that detects genomic copy number variations using microarray technology. - Person: Chris Stoeckert, Jie Zheng - MO_856 comparative_genome_hybridization_design - comparative genome hybridization by array design + A study design that detects genomic copy number variations using microarray technology. + Person: Chris Stoeckert, Jie Zheng + MO_856 comparative_genome_hybridization_design + comparative genome hybridization by array design @@ -35361,13 +35645,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -35375,13 +35669,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-27 production by T cells + assay measuring epitope specific interleukin-27 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|biological activity - biological activity assay measuring epitope specific interleukin-27 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|biological activity + assay measuring epitope specific interleukin-27 production by T cells @@ -35392,9 +35686,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 in vivo design - A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. - Person: Chris Stoeckert, Jie Zheng - MO_454 in_vivo_design + A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. + Person: Chris Stoeckert, Jie Zheng + MO_454 in_vivo_design in vivo design @@ -35404,12 +35698,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - genotyping by high throughput sequencing design + genotyping by high throughput sequencing design - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. - Person: Chris Stoeckert, Jie Zheng - MO_560 genotyping_design - genotyping by high throughput sequencing design + A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. + Person: Chris Stoeckert, Jie Zheng + MO_560 genotyping_design + genotyping by high throughput sequencing design @@ -35429,13 +35723,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific tolerance induction by T cells + epitope specific tolerance induction by T cells - A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific tolerance induction by T cells + A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific tolerance induction by T cells @@ -35450,12 +35744,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - innate behavior design + innate behavior design - A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. - Person: Chris Stoeckert, Jie Zheng - MO_355 innate_behavior_design - innate behavior design + A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. + Person: Chris Stoeckert, Jie Zheng + MO_355 innate_behavior_design + innate behavior design @@ -35466,21 +35760,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells - An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells @@ -35490,12 +35800,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - SNP microarray + SNP microarray - A DNA microarray used to detect polymorphisms in DNA samples - Person: Helen Parkinson - EFO_0002703 SNP array - SNP microarray + A DNA microarray used to detect polymorphisms in DNA samples + Person: Helen Parkinson + EFO_0002703 SNP array + SNP microarray @@ -35526,12 +35836,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - cell component comparison design + cell component comparison design - A study design that compares samples from different cell components. - Person: Chris Stoeckert, Jie Zheng - MO_1019 cell_component_comparison_design - cell component comparison design + A study design that compares samples from different cell components. + Person: Chris Stoeckert, Jie Zheng + MO_1019 cell_component_comparison_design + cell component comparison design @@ -35542,21 +35852,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|ELISPOT + An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|ELISPOT ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -35578,13 +35904,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific macrophage inflammatory protein-1 alpha production by T cells + epitope specific macrophage inflammatory protein-1 alpha production by T cells - A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific macrophage inflammatory protein-1 alpha production by T cells + A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -35604,13 +35930,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific T cell activation + epitope specific T cell activation - A process of T cell activation resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific T cell activation + A process of T cell activation resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific T cell activation @@ -35621,13 +35947,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -35635,13 +35971,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-10 production by T cells + assay measuring epitope specific interleukin-10 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|biological activity - biological activity assay measuring epitope specific interleukin-10 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|biological activity + assay measuring epitope specific interleukin-10 production by T cells @@ -35652,21 +35988,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells - An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|cytometric bead array + A cytometric bead array assay that detects transforming growth factor-beta production by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|cytometric bead array cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells @@ -35676,12 +36028,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - ex vivo design + ex vivo design - A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. - Person: Chris Stoeckert, Jie Zheng - MO_808 ex_vivo_design - ex vivo design + A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. + Person: Chris Stoeckert, Jie Zheng + MO_808 ex_vivo_design + ex vivo design @@ -35701,13 +36053,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific type IV hypersensitivity by T cells + epitope specific type IV hypersensitivity by T cells - A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific type IV hypersensitivity by T cells + A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific type IV hypersensitivity by T cells @@ -35738,12 +36090,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - normalization testing design + normalization testing design - A study design that tests different normalization procedures. - Person: Chris Stoeckert, Jie Zheng - MO_729 normalization_testing_design - normalization testing design + A study design that tests different normalization procedures. + Person: Chris Stoeckert, Jie Zheng + MO_729 normalization_testing_design + normalization testing design @@ -35765,10 +36117,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 intracellular material detection assay measuring epitope specific perforin release - A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - perforin release|intracellular staining + A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + perforin release|intracellular staining intracellular material detection assay measuring epitope specific perforin release @@ -35780,21 +36132,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells @@ -35806,13 +36174,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -35820,13 +36198,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-22 production by T cells + assay measuring epitope specific interleukin-22 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|biological activity - biological activity assay measuring epitope specific interleukin-22 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|biological activity + assay measuring epitope specific interleukin-22 production by T cells @@ -35837,13 +36215,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -35851,13 +36239,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-8 production by T cells + assay measuring epitope specific interleukin-8 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-8 release|biological activity - biological activity assay measuring epitope specific interleukin-8 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-8 release|biological activity + assay measuring epitope specific interleukin-8 production by T cells @@ -35878,13 +36266,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific chemokine (C-C motif) ligand 1 production by T cells + epitope specific chemokine (C-C motif) ligand 1 production by T cells - A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific chemokine (C-C motif) ligand 1 production by T cells + A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -35895,21 +36283,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells - An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells @@ -35945,9 +36349,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 ChIP-chip by SNP array assay - A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin - ArrayExpress production team - EFO:0002764 + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin + ArrayExpress production team + EFO:0002764 ChIP-chip by SNP array assay @@ -35959,21 +36363,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific RANTES production by T cells - An assay of epitope specific RANTES production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|ELISA + An enzyme-linked immunosorbent assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|ELISA ELISA measuring epitope specific RANTES production by T cells @@ -35985,21 +36405,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells - An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|cytometric bead array + A cytometric bead array assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells @@ -36037,12 +36473,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - environmental history design + environmental history design - A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. - Person: Chris Stoeckert, Jie Zheng - MO_698 environmental_history_design - environmental history design + A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. + Person: Chris Stoeckert, Jie Zheng + MO_698 environmental_history_design + environmental history design @@ -36053,21 +36489,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-6 production by T cells - An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-6 production by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-6 production by T cells @@ -36095,10 +36547,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. - IEDB - IEDB - antibody help|biological activity + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. + IEDB + IEDB + antibody help|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response @@ -36110,10 +36562,19 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + @@ -36127,13 +36588,14 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 + plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|surface plasmon resonance (SPR)|nM + A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|surface plasmon resonance (SPR)|nM plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex @@ -36145,13 +36607,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -36159,13 +36631,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-5 production by T cells + assay measuring epitope specific interleukin-5 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|biological activity - biological activity assay measuring epitope specific interleukin-5 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|biological activity + assay measuring epitope specific interleukin-5 production by T cells @@ -36176,21 +36648,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific transforming growth factor-beta production by T cells - An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|ELISA + An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|ELISA ELISA measuring epitope specific transforming growth factor-beta production by T cells @@ -36202,13 +36690,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -36216,13 +36714,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific RANTES production by T cells + assay measuring epitope specific RANTES production by T cells - A T cell epitope specific cytokine production assay that detects RANTES production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|biological activity - biological activity assay measuring epitope specific RANTES production by T cells + A T cell epitope specific cytokine production assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|biological activity + assay measuring epitope specific RANTES production by T cells @@ -36233,13 +36731,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -36247,13 +36755,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells + assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells - A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|biological activity - biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells + A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|biological activity + assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells @@ -36302,9 +36810,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 transcription profiling by tiling array assay - A transcription profiling by array assay that uses a tiling path array. - James Malone - EFO:0002769 + A transcription profiling by array assay that uses a tiling path array. + James Malone + EFO:0002769 transcription profiling by tiling array assay @@ -36316,21 +36824,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-22 production by T cells - An assay of epitope specific interleukin-22 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|ELISA ELISA measuring epitope specific interleukin-22 production by T cells @@ -36342,13 +36866,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -36356,13 +36890,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-21 production by T cells + assay measuring epitope specific interleukin-21 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|biological activity - biological activity assay measuring epitope specific interleukin-21 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|biological activity + assay measuring epitope specific interleukin-21 production by T cells @@ -36373,21 +36907,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-9 production by T cells - An assay of epitope specific interleukin-9 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-9 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-9 release|ELISA ELISA measuring epitope specific interleukin-9 production by T cells @@ -36405,9 +36955,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 transcription profiling by high throughput sequencing design - A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team + A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team transcription profiling by high throughput sequencing design @@ -36419,21 +36969,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells - An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ICS + A flow cytometry assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells @@ -36445,21 +37011,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells - An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells @@ -36471,10 +37053,25 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + @@ -36483,10 +37080,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells - A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells @@ -36498,21 +37095,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|cytometric bead array + A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|cytometric bead array cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells @@ -36524,21 +37137,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-23 production by T cells - An assay of epitope specific interleukin-23 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|ELISA ELISA measuring epitope specific interleukin-23 production by T cells @@ -36561,10 +37190,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release - A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - perforin release|RNA/DNA detection + A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + perforin release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release @@ -36576,21 +37205,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|ELISA + An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|ELISA ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -36626,9 +37271,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 genotyping by high throughput sequencing assay - A genotyping assay that uses a high througput sequencer - James Malone - EFO:0002771 + A genotyping assay that uses a high througput sequencer + James Malone + EFO:0002771 genotyping by high throughput sequencing assay @@ -36673,11 +37318,11 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 ChIP-chip assay - An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin - Bjoern Petesr - James Malone - ChIP-on-chip assay - url:http://en.wikipedia.org/wiki/ChIP-on-chip + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin + Bjoern Petesr + James Malone + ChIP-on-chip assay + url:http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip assay @@ -36699,13 +37344,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific T cell tolerance induction + epitope specific T cell tolerance induction - A process of T cell tolerance induction resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific T cell tolerance induction + A process of T cell tolerance induction resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific T cell tolerance induction @@ -36716,12 +37361,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation - An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - T cell degranulation by intracellular staining + T cell degranulation by intracellular staining obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation true @@ -36734,13 +37379,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -36748,13 +37403,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-13 production by T cells + assay measuring epitope specific interleukin-13 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|biological activity - biological activity assay measuring epitope specific interleukin-13 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|biological activity + assay measuring epitope specific interleukin-13 production by T cells @@ -36785,12 +37440,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - array platform variation design + array platform variation design - A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. - Person: Chris Stoeckert, Jie Zheng - MO_899 array_platform_variation_design - array platform variation design + A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. + Person: Chris Stoeckert, Jie Zheng + MO_899 array_platform_variation_design + array platform variation design @@ -36801,13 +37456,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -36815,13 +37480,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring interleukin-9 production by T cells + assay measuring interleukin-9 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-9 release|biological activity - biological activity assay measuring interleukin-9 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-9 release|biological activity + assay measuring interleukin-9 production by T cells @@ -36842,13 +37507,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-3 production by T cells + epitope specific interleukin-3 production by T cells - A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-3 production by T cells + A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-3 production by T cells @@ -36859,21 +37524,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells - An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells @@ -36895,13 +37576,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific lymphotoxin A production by T cells + epitope specific lymphotoxin A production by T cells - A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific lymphotoxin A production by T cells + A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific lymphotoxin A production by T cells @@ -36922,13 +37603,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-1 alpha production by T cells + epitope specific interleukin-1 alpha production by T cells - A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-1 alpha production by T cells + A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-1 alpha production by T cells @@ -36949,12 +37630,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - ChIP-seq design + ChIP-seq design - A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. - Person: Chris Stoeckert, Jie Zheng - http://en.wikipedia.org/wiki/Chip-Sequencing - ChIP-seq design + A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. + Person: Chris Stoeckert, Jie Zheng + http://en.wikipedia.org/wiki/Chip-Sequencing + ChIP-seq design @@ -36969,12 +37650,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - translational bias design + translational bias design - A study design that characterizes the association of transcripts and translation machinery. - Person: Chris Stoeckert, Jie Zheng - MO_939 translational_bias_design - translational bias design + A study design that characterizes the association of transcripts and translation machinery. + Person: Chris Stoeckert, Jie Zheng + MO_939 translational_bias_design + translational bias design @@ -36985,21 +37666,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-3 production by T cells - An assay of epitope specific interleukin-3 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|ELISA ELISA measuring epitope specific interleukin-3 production by T cells @@ -37011,21 +37708,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-1 alpha production by T cells - An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|ELISA ELISA measuring epitope specific interleukin-1 alpha production by T cells @@ -37047,13 +37760,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-27 production by T cells + epitope specific interleukin-27 production by T cells - A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-27 production by T cells + A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-27 production by T cells @@ -37080,10 +37793,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - T cell help|biological activity + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + T cell help|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response @@ -37095,13 +37808,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -37109,13 +37832,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific transforming growth factor-beta production by T cells + assay measuring epitope specific transforming growth factor-beta production by T cells - A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|biological activity - biological activity assay measuring epitope specific transforming growth factor-beta production by T cells + A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|biological activity + assay measuring epitope specific transforming growth factor-beta production by T cells @@ -37124,13 +37847,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - FWER adjusted p-value + FWER adjusted p-value http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests PERS:Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) - FWER adjusted p-value + FWER adjusted p-value @@ -37165,11 +37888,11 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 DNA methylation profiling by high throughput sequencing assay - A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology - ArrayExpress production team - Helen Parkinson - James Malone - EFO:0002761 + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology + ArrayExpress production team + Helen Parkinson + James Malone + EFO:0002761 DNA methylation profiling by high throughput sequencing assay @@ -37191,13 +37914,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific transforming growth factor-beta production by T cells + epitope specific transforming growth factor-beta production by T cells - A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific transforming growth factor-beta production by T cells + A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific transforming growth factor-beta production by T cells @@ -37208,21 +37931,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells - An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells @@ -37250,10 +37989,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 biological activity assay measuring epitope specific cytotoxic T cell degranulation - A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - degranulation|biological activity + A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + degranulation|biological activity biological activity assay measuring epitope specific cytotoxic T cell degranulation @@ -37265,21 +38004,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells - An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|bioassay + A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|bioassay cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells @@ -37302,10 +38057,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 RNA-seq assay - An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. - James Malone - transcription profiling by high throughput sequencing - EFO:0002770 + An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + James Malone + transcription profiling by high throughput sequencing + EFO:0002770 RNA-seq assay @@ -37317,21 +38072,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|ELISPOT + An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|ELISPOT ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -37343,21 +38114,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells - An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells @@ -37394,9 +38181,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 genotyping by array assay - A genotyping assay that uses an array - ArrayExpress production team - EFO:0002767 + A genotyping assay that uses an array + ArrayExpress production team + EFO:0002767 genotyping by array assay @@ -37418,13 +38205,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-16 production by T cells + epitope specific interleukin-16 production by T cells - A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-16 production by T cells + A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-16 production by T cells @@ -37435,13 +38222,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -37449,13 +38246,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -37466,21 +38263,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells @@ -37496,12 +38309,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - DNA methylation profiling by array design + DNA methylation profiling by array design - A study design in which the methylation state of DNA is determined and is compared between samples using array technology. - Person: Chris Stoeckert, Jie Zheng - GROUP: ArrayExpress production team - DNA methylation profiling by array design + A study design in which the methylation state of DNA is determined and is compared between samples using array technology. + Person: Chris Stoeckert, Jie Zheng + GROUP: ArrayExpress production team + DNA methylation profiling by array design @@ -37512,21 +38325,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells - An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells @@ -37538,13 +38367,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -37552,13 +38391,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-16 production by T cells + assay measuring epitope specific interleukin-16 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|biological activity - biological activity assay measuring epitope specific interleukin-16 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|biological activity + assay measuring epitope specific interleukin-16 production by T cells @@ -37569,21 +38408,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific IP-10 production by T cells - An assay of epitope specific IP-10 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|ELISA + An enzyme-linked immunosorbent assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|ELISA ELISA measuring epitope specific IP-10 production by T cells @@ -37601,9 +38456,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 translation profiling assay - An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. - James Malone - EFO:0001033 + An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. + James Malone + EFO:0001033 translation profiling assay @@ -37615,21 +38470,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-15 production by T cells - An assay of epitope specific interleukin-15 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|ELISA ELISA measuring epitope specific interleukin-15 production by T cells @@ -37641,21 +38512,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-12 production by T cells - An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|cytometric bead array + A cytometric bead array assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-12 production by T cells @@ -37665,12 +38552,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - in vitro design + in vitro design - A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. - Person: Chris Stoeckert, Jie Zheng - MO_347 in_vitro_design - in vitro design + A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. + Person: Chris Stoeckert, Jie Zheng + MO_347 in_vitro_design + in vitro design @@ -37685,12 +38572,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - RNAi profiling by array design + RNAi profiling by array design - A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - RNAi profiling by array design + A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + RNAi profiling by array design @@ -37701,10 +38588,25 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + @@ -37713,10 +38615,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 ELISA measuring epitope specific lymphotoxin A production by T cells - An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - lymphotoxin A/TNFb release|ELISA + An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + lymphotoxin A/TNFb release|ELISA ELISA measuring epitope specific lymphotoxin A production by T cells @@ -37728,21 +38630,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-5 production by T cells - An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|cytometric bead array + A cytometric bead array assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-5 production by T cells @@ -37758,12 +38676,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - transcription profiling by array design + transcription profiling by array design - A study design that identifies forms and abundance of transcripts in the genome using microarray technology. - Person: Chris Stoeckert, Jie Zheng - MO_533 transcript_identification_design - transcription profiling by array design + A study design that identifies forms and abundance of transcripts in the genome using microarray technology. + Person: Chris Stoeckert, Jie Zheng + MO_533 transcript_identification_design + transcription profiling by array design @@ -37774,21 +38692,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells - An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells @@ -37800,13 +38734,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -37814,13 +38758,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-15 production by T cells + assay measuring epitope specific interleukin-15 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|biological activity - biological activity assay measuring epitope specific interleukin-15 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|biological activity + assay measuring epitope specific interleukin-15 production by T cells @@ -37851,12 +38795,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - disease state design + disease state design - A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. - Person: Chris Stoeckert, Jie Zheng - MO_902 disease_state_design - disease state design + A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. + Person: Chris Stoeckert, Jie Zheng + MO_902 disease_state_design + disease state design @@ -37883,13 +38827,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -37897,13 +38851,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-17 production by T cells + assay measuring epitope specific interleukin-17 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|biological activity - biological activity assay measuring epitope specific interleukin-17 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|biological activity + assay measuring epitope specific interleukin-17 production by T cells @@ -37914,21 +38868,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-17 production by T cells - An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|cytometric bead array + A cytometric bead array assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17 production by T cells @@ -37940,21 +38910,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-10 production by T cells - An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-10 release|cytometric bead array + A cytometric bead array assay that detects interleukin-10 production by T cells. + IEDB + IEDB + IL-10 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-10 production by T cells @@ -37966,21 +38952,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells - An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells @@ -37992,21 +38994,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells - An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ICS + A flow cytometry assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells @@ -38018,21 +39036,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|cytometric bead array + A cytometric bead array assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-2 production by T cells @@ -38044,21 +39078,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells - An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells @@ -38070,21 +39120,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|ELISA + An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -38096,21 +39162,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|ICS + A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|ICS intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -38176,9 +39258,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 RNAi profiling by array assay - An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. - James Malone - EFO:0001030 + An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. + James Malone + EFO:0001030 RNAi profiling by array assay @@ -38234,12 +39316,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - RNA stability design + RNA stability design - A study design that examines the stability and/or decay of RNA transcripts. - Person: Chris Stoeckert, Jie Zheng - MO_553 RNA_stability_design - RNA stability design + A study design that examines the stability and/or decay of RNA transcripts. + Person: Chris Stoeckert, Jie Zheng + MO_553 RNA_stability_design + RNA stability design @@ -38248,13 +39330,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - tiling microarray + tiling microarray - A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. - Person: Helen Parkinson - genome tiling array - EFO_0002704: tiling array - tiling microarray + A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. + Person: Helen Parkinson + genome tiling array + EFO_0002704: tiling array + tiling microarray @@ -38265,13 +39347,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -38279,13 +39371,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific IP-10 production by T cells + assay measuring epitope specific IP-10 production by T cells - A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|biological activity - biological activity assay measuring epitope specific IP-10 production by T cells + A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|biological activity + assay measuring epitope specific IP-10 production by T cells @@ -38296,21 +39388,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells - An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ICS + A flow cytometry assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells @@ -38342,12 +39450,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - species comparison design + species comparison design - A study design that assays differences between distinct species. - Person: Chris Stoeckert, Jie Zheng - MO_675 species_design - species comparison design + A study design that assays differences between distinct species. + Person: Chris Stoeckert, Jie Zheng + MO_675 species_design + species comparison design @@ -38358,10 +39466,19 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + @@ -38375,13 +39492,14 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 + X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex - A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|x-ray crystallography|angstroms + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex @@ -38397,12 +39515,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - transcription profiling by RT-PCR design + transcription profiling by RT-PCR design - A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - transcription profiling by RT-PCR design + A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + transcription profiling by RT-PCR design @@ -38422,13 +39540,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific T cell enhancement of B cell mediated immune response + epitope specific T cell enhancement of B cell mediated immune response - A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific T cell enhancement of B cell mediated immune response + A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific T cell enhancement of B cell mediated immune response @@ -38439,21 +39557,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|ELISA + An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -38475,13 +39609,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-21 production by T cells + epitope specific interleukin-21 production by T cells - A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-21 production by T cells + A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-21 production by T cells @@ -38492,21 +39626,31 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex - A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - T cell- APC binding|binding assay + A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + T cell- APC binding|binding assay flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex @@ -38589,9 +39733,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 proteomic profiling by array assay - An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. - James Malone - EFO:0002765 + An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. + James Malone + EFO:0002765 proteomic profiling by array assay @@ -38603,21 +39747,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|bioassay + A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|bioassay cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells @@ -38640,10 +39800,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 ELISPOT assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|ELISPOT + A T cell epitope specific granzyme B release assay that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|ELISPOT ELISPOT assay measuring epitope specific granzyme B release by T cells @@ -38659,12 +39819,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - microRNA profiling by array design + microRNA profiling by array design - A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - microRNA profiling by array design + A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + microRNA profiling by array design @@ -38695,10 +39855,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 in vivo assay measuring T cell epitope specific tolerance induction - An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - tolerance|in vivo assay + An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + tolerance|in vivo assay in vivo assay measuring T cell epitope specific tolerance induction @@ -38710,21 +39870,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells - An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - CCL5/RANTES release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. + IEDB + IEDB + CCL5/RANTES release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells @@ -38736,21 +39912,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-4 production by T cells - An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|cytometric bead array + A cytometric bead array assay that detects interleukin-4 production by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-4 production by T cells @@ -38762,13 +39954,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -38776,13 +39978,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific lymphotoxin A production by T cells + assay measuring epitope specific lymphotoxin A production by T cells - A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - lymphotoxin A/TNFb release|biological activity - biological activity assay measuring epitope specific lymphotoxin A production by T cells + A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + lymphotoxin A/TNFb release|biological activity + assay measuring epitope specific lymphotoxin A production by T cells @@ -38817,12 +40019,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - organism development design + organism development design - A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. - Person: Chris Stoeckert, Jie Zheng - MO_892 development_or_differentiation_design - organism development design + A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. + Person: Chris Stoeckert, Jie Zheng + MO_892 development_or_differentiation_design + organism development design @@ -38837,12 +40039,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - family history design + family history design - A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. - Person: Chris Stoeckert, Jie Zheng - MO_544 family_history_design - family history design + A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. + Person: Chris Stoeckert, Jie Zheng + MO_544 family_history_design + family history design @@ -38853,21 +40055,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA. - IEDB - IEDB - CXCL9/MIG release|ELISA + An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + IEDB + IEDB + CXCL9/MIG release|ELISA ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -38917,9 +40135,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 DNA methylation profiling by array assay - A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology - James Malone - EFO:0002759 + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology + James Malone + EFO:0002759 DNA methylation profiling by array assay @@ -38931,13 +40149,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -38945,13 +40173,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|biological activity - biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|biological activity + assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -38972,13 +40200,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific granulocyte colony stimulating factor production by T cells + epitope specific granulocyte colony stimulating factor production by T cells - A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific granulocyte colony stimulating factor production by T cells + A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific granulocyte colony stimulating factor production by T cells @@ -39076,9 +40304,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 microRNA profiling by array assay - An assay that analyses the microRNA component of the transcriptome using a microRNA array. - James Malone - EFO:0000753 + An assay that analyses the microRNA component of the transcriptome using a microRNA array. + James Malone + EFO:0000753 microRNA profiling by array assay @@ -39088,12 +40316,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - quality control testing design + quality control testing design - A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. - Person: Chris Stoeckert, Jie Zheng - MO_981 quality_control_testing_design - quality control testing design + A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. + Person: Chris Stoeckert, Jie Zheng + MO_981 quality_control_testing_design + quality control testing design @@ -39118,12 +40346,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - clinical history design + clinical history design - A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. - Person: Chris Stoeckert, Jie Zheng - MO_832 clinical_history_design - clinical history design + A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. + Person: Chris Stoeckert, Jie Zheng + MO_832 clinical_history_design + clinical history design @@ -39134,21 +40362,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells - An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells @@ -39160,21 +40404,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|bioassay + A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|bioassay cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -39186,21 +40446,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells - An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|ICS + A flow cytometry assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells @@ -39212,21 +40488,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells @@ -39238,21 +40530,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells - An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|ELISA + An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|ELISA ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells @@ -39264,13 +40572,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -39278,13 +40596,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -39295,21 +40613,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-21 production by T cells - An assay of epitope specific interleukin-21 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|ELISA ELISA measuring epitope specific interleukin-21 production by T cells @@ -39337,10 +40671,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity - An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - type IV hypersensitivity (DTH)|in vivo skin test + An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + type IV hypersensitivity (DTH)|in vivo skin test in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity @@ -39352,21 +40686,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-13 production by T cells - An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|cytometric bead array + A cytometric bead array assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-13 production by T cells @@ -39378,21 +40728,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells @@ -39414,13 +40780,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific tumor necrosis factor superfamily cytokine production by T cells + epitope specific tumor necrosis factor superfamily cytokine production by T cells - A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific tumor necrosis factor superfamily cytokine production by T cells + A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -39449,7 +40815,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng - MO_58 Allele + MO_58 Allele allele information @@ -39461,10 +40827,25 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + @@ -39473,10 +40854,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells - A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|cytometric bead array + A cytometric bead array assay that detects tumor necrosis factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells @@ -39488,21 +40869,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-17 production by T cells - An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17 production by T cells @@ -39514,21 +40911,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells - An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells @@ -39540,21 +40953,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -39586,13 +41015,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - post-transcriptional modification design + post-transcriptional modification design - A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. - post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases - Person: Chris Stoeckert, Jie Zheng - MO_392 cellular_modification_design - post-transcriptional modification design + A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. + post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases + Person: Chris Stoeckert, Jie Zheng + MO_392 cellular_modification_design + post-transcriptional modification design @@ -39603,21 +41032,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-8 production by T cells - An assay of epitope specific interleukin-8 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-8 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-8 release|ELISA ELISA measuring epitope specific interleukin-8 production by T cells @@ -39629,21 +41074,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-6 production by T cells - An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|cytometric bead array + A cytometric bead array assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-6 production by T cells @@ -39686,9 +41147,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 transcription profiling by RT-PCR assay - A transcription profiling assay that uses reverse transcription PCR (RT-PCR). - Anna Farne - EFO:0002943 + A transcription profiling assay that uses reverse transcription PCR (RT-PCR). + Anna Farne + EFO:0002943 transcription profiling by RT-PCR assay @@ -39710,13 +41171,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific chemokine (C-C motif) ligand 4 production by T cells + epitope specific chemokine (C-C motif) ligand 4 production by T cells - A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific chemokine (C-C motif) ligand 4 production by T cells + A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -39727,13 +41188,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -39741,13 +41212,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-23 production by T cells + assay measuring epitope specific interleukin-23 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|biological activity - biological activity assay measuring epitope specific interleukin-23 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|biological activity + assay measuring epitope specific interleukin-23 production by T cells @@ -39787,12 +41258,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - cellular process design + cellular process design - A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - Person: Chris Stoeckert, Jie Zheng - MO_810 cellular_process_design - cellular process design + A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + Person: Chris Stoeckert, Jie Zheng + MO_810 cellular_process_design + cellular process design @@ -39813,13 +41284,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific RANTES production by T cells + epitope specific RANTES production by T cells - A process of RANTES production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific RANTES production by T cells + A process of RANTES production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific RANTES production by T cells @@ -39830,21 +41301,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells - An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells @@ -39856,21 +41343,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|cytometric bead array + A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -39897,21 +41400,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|ICS + A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -39932,13 +41451,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific granzyme B production by T cells + epitope specific granzyme B production by T cells - A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific granzyme B production by T cells + A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific granzyme B production by T cells @@ -39959,13 +41478,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-8 production by T cells + epitope specific interleukin-8 production by T cells - A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-8 production by T cells + A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-8 production by T cells @@ -39980,12 +41499,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - injury design + injury design - A study design in which the response of an organism(s) to injury or damage is studied. - Person: Chris Stoeckert, Jie Zheng - MO_726 injury_design - injury design + A study design in which the response of an organism(s) to injury or damage is studied. + Person: Chris Stoeckert, Jie Zheng + MO_726 injury_design + injury design @@ -39996,21 +41515,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells - An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|ICS + A flow cytometry assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells @@ -40054,12 +41589,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - organism status comparison design + organism status comparison design - A study design that compares samples from live and dead organisms. - Person: Chris Stoeckert, Jie Zheng - MO_841 organism_status_design - organism status comparison design + A study design that compares samples from live and dead organisms. + Person: Chris Stoeckert, Jie Zheng + MO_841 organism_status_design + organism status comparison design @@ -40070,21 +41605,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|ELISA + An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -40096,21 +41647,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|cytometric bead array + A cytometric bead array assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|cytometric bead array cytometric bead array assay measuring epitope specific interferon-gamma production by T cells @@ -40122,13 +41689,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -40136,13 +41713,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-18 production by T cells + assay measuring epitope specific interleukin-18 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|biological activity - biological activity assay measuring epitope specific interleukin-18 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|biological activity + assay measuring epitope specific interleukin-18 production by T cells @@ -40163,13 +41740,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-23 production by T cells + epitope specific interleukin-23 production by T cells - A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-23 production by T cells + A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-23 production by T cells @@ -40180,21 +41757,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells - An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells @@ -40206,21 +41799,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells - An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells @@ -40232,21 +41841,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells - An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells @@ -40258,21 +41883,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|ICS + A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -40294,13 +41935,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific monocyte chemotactic protein-1 production by T cells + epitope specific monocyte chemotactic protein-1 production by T cells - A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific monocyte chemotactic protein-1 production by T cells + A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific monocyte chemotactic protein-1 production by T cells @@ -40309,12 +41950,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - genotyping by array design + genotyping by array design - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. - Person: Chris Stoeckert, Jie Zheng - MO_560 genotyping_design - genotyping by array design + A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. + Person: Chris Stoeckert, Jie Zheng + MO_560 genotyping_design + genotyping by array design @@ -40325,13 +41966,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -40339,13 +41990,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-1 alpha production by T cells + assay measuring epitope specific interleukin-1 alpha production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|biological activity - biological activity assay measuring epitope specific interleukin-1 alpha production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|biological activity + assay measuring epitope specific interleukin-1 alpha production by T cells @@ -40356,21 +42007,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells - An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells @@ -40382,13 +42049,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -40396,13 +42073,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interferon-beta production by T cells + assay measuring epitope specific interferon-beta production by T cells - A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|biological activity - biological activity assay measuring epitope specific interferon-beta production by T cells + A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|biological activity + assay measuring epitope specific interferon-beta production by T cells @@ -40413,13 +42090,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -40427,13 +42114,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific interleukin-12 production by T cells + assay measuring epitope specific interleukin-12 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|biological activity - biological activity assay measuring epitope specific interleukin-12 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|biological activity + assay measuring epitope specific interleukin-12 production by T cells @@ -40455,10 +42142,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 in vivo assay measuring epitope specific T cell killing - A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - cytotoxicity|in vivo assay + A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + cytotoxicity|in vivo assay in vivo assay measuring epitope specific T cell killing @@ -40547,10 +42234,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 comparative genomic hybridization by array assay - An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. - James Malone - array CGH - EFO:0000749 + An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. + James Malone + array CGH + EFO:0000749 comparative genomic hybridization by array assay @@ -40571,13 +42258,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific cytotoxic T cell degranulation + epitope specific cytotoxic T cell degranulation - A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific cytotoxic T cell degranulation + A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific cytotoxic T cell degranulation @@ -40588,21 +42275,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells - An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells @@ -40644,12 +42347,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - stimulus or stress design + stimulus or stress design - A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. - Person: Chris Stoeckert, Jie Zheng - MO_568 stimulus_or_stress_design - stimulus or stress design + A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. + Person: Chris Stoeckert, Jie Zheng + MO_568 stimulus_or_stress_design + stimulus or stress design @@ -40660,21 +42363,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells - An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|cytometric bead array + A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|cytometric bead array cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells @@ -40710,13 +42429,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-22 production by T cells + epitope specific interleukin-22 production by T cells - A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-22 production by T cells + A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-22 production by T cells @@ -40727,13 +42446,23 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + @@ -40741,13 +42470,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|biological activity - biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|biological activity + assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -40762,12 +42491,12 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - protocol optimization design + protocol optimization design - A study design where different protocols or protocol parameters are compared aims to find an optimized protocol - Person: Chris Stoeckert, Jie Zheng - MO_934 optimization_design - protocol optimization design + A study design where different protocols or protocol parameters are compared aims to find an optimized protocol + Person: Chris Stoeckert, Jie Zheng + MO_934 optimization_design + protocol optimization design @@ -40778,21 +42507,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + + + + + + + + + + + + + + + + + promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay. - IEDB - IEDB - IL-2 release|reporter gene assay + A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. + IEDB + IEDB + IL-2 release|reporter gene assay promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells @@ -40824,13 +42569,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - ChIP-chip design + ChIP-chip design - A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. - Person: Chris Stoeckert, Jie Zheng - ChIP-on-chip design - MO_933 binding_site_identification_design - ChIP-chip design + A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. + Person: Chris Stoeckert, Jie Zheng + ChIP-on-chip design + MO_933 binding_site_identification_design + ChIP-chip design @@ -40899,21 +42644,37 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|cytometric bead array + A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -40925,13 +42686,23 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - + + + + + + + + + + + @@ -40939,13 +42710,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - biological activity assay measuring epitope specific interleukin-3 production by T cells + assay measuring epitope specific interleukin-3 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|biological activity - biological activity assay measuring epitope specific interleukin-3 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|biological activity + assay measuring epitope specific interleukin-3 production by T cells @@ -40956,10 +42727,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) biological activity assay measuring epitope specific T cell activation - A T cell epitope dependent biological activity assay that detects T cell activation. - IEDB - IEDB - activation|biological activity + A T cell epitope dependent biological activity assay that detects T cell activation. + IEDB + IEDB + activation|biological activity biological activity assay measuring epitope specific T cell activation @@ -40975,12 +42746,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - imprinting design + imprinting design - A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. - Person: Chris Stoeckert, Jie Zheng - MO_914 imprinting_design - imprinting design + A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. + Person: Chris Stoeckert, Jie Zheng + MO_914 imprinting_design + imprinting design @@ -41005,12 +42776,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - cell cycle design + cell cycle design - A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. - Person: Chris Stoeckert, Jie Zheng - MO_822 cell_cycle_design - cell cycle design + A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. + Person: Chris Stoeckert, Jie Zheng + MO_822 cell_cycle_design + cell cycle design @@ -41025,12 +42796,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - translation profiling design + translation profiling design - A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - translation profiling design + A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + translation profiling design @@ -41061,12 +42832,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - cell type comparison design + cell type comparison design - A study design that compares cells of different type, for example different cell lines. - Person: Chris Stoeckert, Jie Zheng - MO_764 cell_type_comparison_design - cell type comparison design + A study design that compares cells of different type, for example different cell lines. + Person: Chris Stoeckert, Jie Zheng + MO_764 cell_type_comparison_design + cell type comparison design @@ -41077,21 +42848,37 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific RANTES production by T cells - An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|cytometric bead array + A cytometric bead array assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|cytometric bead array cytometric bead array assay measuring epitope specific RANTES production by T cells @@ -41103,21 +42890,37 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells - An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|bioassay + A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells @@ -41129,13 +42932,23 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - + + + + + + + + + + + @@ -41143,13 +42956,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - biological activity assay measuring epitope specific interferon-gamma production by T cells + assay measuring epitope specific interferon-gamma production by T cells - A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|biological activity - biological activity assay measuring epitope specific interferon-gamma production by T cells + A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|biological activity + assay measuring epitope specific interferon-gamma production by T cells @@ -41170,13 +42983,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - epitope specific interleukin-9 production by T cells + epitope specific interleukin-9 production by T cells - A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-9 production by T cells + A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-9 production by T cells @@ -41187,13 +43000,23 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - + + + + + + + + + + + @@ -41201,13 +43024,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - biological activity assay measuring epitope specific tumor necrosis factor production by T cells + assay measuring epitope specific tumor necrosis factor production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|biological activity - biological activity assay measuring epitope specific tumor necrosis factor production by T cells + An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|biological activity + assay measuring epitope specific tumor necrosis factor production by T cells @@ -41216,12 +43039,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - ChIP-chip by tiling array design + ChIP-chip by tiling array design - A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - ChIP-chip by tiling array design + A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + ChIP-chip by tiling array design @@ -41285,12 +43108,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - dose response design + dose response design - A study design that examines the relationship between the size of the administered dose and the extent of the response. - Person: Chris Stoeckert, Jie Zheng - MO_485 dose_response_design - dose response design + A study design that examines the relationship between the size of the administered dose and the extent of the response. + Person: Chris Stoeckert, Jie Zheng + MO_485 dose_response_design + dose response design @@ -41325,9 +43148,9 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) ChIP-chip by tiling array assay - A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin - ArrayExpress production team - EFO:0002762 + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin + ArrayExpress production team + EFO:0002762 ChIP-chip by tiling array assay @@ -41348,13 +43171,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - epitope specific helper T cell enhancement of T cell mediated immune response + epitope specific helper T cell enhancement of T cell mediated immune response - A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific helper T cell enhancement of T cell mediated immune response + A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific helper T cell enhancement of T cell mediated immune response @@ -41375,13 +43198,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - epitope specific interferon-beta production by T cells + epitope specific interferon-beta production by T cells - A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interferon-beta production by T cells + A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interferon-beta production by T cells @@ -41412,12 +43235,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - organism part comparison design + organism part comparison design - A study design that compares tissues, regions, organs within or between organisms - Person: Chris Stoeckert, Jie Zheng - MO_953 organism_part_comparison_design - organism part comparison design + A study design that compares tissues, regions, organs within or between organisms + Person: Chris Stoeckert, Jie Zheng + MO_953 organism_part_comparison_design + organism part comparison design @@ -41439,10 +43262,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) intracellular material detection measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|intracellular staining + A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|intracellular staining intracellular material detection measuring epitope specific granzyme B release by T cells @@ -41458,12 +43281,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - protein binding site identification design + protein binding site identification design - A study design that investigates protein binding sites on nucleic acids. - Person: Chris Stoeckert, Jie Zheng - MO_933 binding_site_identification_design - protein binding site identification design + A study design that investigates protein binding sites on nucleic acids. + Person: Chris Stoeckert, Jie Zheng + MO_933 binding_site_identification_design + protein binding site identification design @@ -41494,12 +43317,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - sex comparison design + sex comparison design - A study design that assays differences associated with an organism's sex, gender or mating type. - Person: Chris Stoeckert, Jie Zheng - MO_575 sex_design - sex comparison design + A study design that assays differences associated with an organism's sex, gender or mating type. + Person: Chris Stoeckert, Jie Zheng + MO_575 sex_design + sex comparison design @@ -41514,12 +43337,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - transcription profiling by tiling array design + transcription profiling by tiling array design - A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. - Person: Chris Stoeckert, Jie Zheng - MO_507 tiling_path_design - transcription profiling by tiling array design + A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. + Person: Chris Stoeckert, Jie Zheng + MO_507 tiling_path_design + transcription profiling by tiling array design @@ -41544,12 +43367,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - cell differentiation design + cell differentiation design - A study design that assays events associated with cell development or differentiation. - Person: Chris Stoeckert, Jie Zheng - MO_892 development_or_differentiation_design - cell differentiation design + A study design that assays events associated with cell development or differentiation. + Person: Chris Stoeckert, Jie Zheng + MO_892 development_or_differentiation_design + cell differentiation design @@ -41558,12 +43381,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - transcription profiling design + transcription profiling design - A study design that identifies forms and abundance of transcripts in the genome. - Person: Chris Stoeckert, Jie Zheng - MO_533 transcript_identification_design - transcription profiling design + A study design that identifies forms and abundance of transcripts in the genome. + Person: Chris Stoeckert, Jie Zheng + MO_533 transcript_identification_design + transcription profiling design @@ -41578,12 +43401,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - operon identification design + operon identification design - A study design that identifies locations and members of operons in a genome. - Person: Chris Stoeckert, Jie Zheng - MO_772 operon_identification_design - operon identification design + A study design that identifies locations and members of operons in a genome. + Person: Chris Stoeckert, Jie Zheng + MO_772 operon_identification_design + operon identification design @@ -41594,21 +43417,37 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + radio immuno assay measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|radio immuno assay (RIA) + A radio immuno assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|radio immuno assay (RIA) radio immuno assay measuring epitope specific interferon-gamma production by T cells @@ -41624,12 +43463,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - DNA methylation profiling by high throughput sequencing design + DNA methylation profiling by high throughput sequencing design - A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. - Person: Chris Stoeckert, Jie Zheng - GROUP: ArrayExpress production team - DNA methylation profiling by high throughput sequencing design + A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. + Person: Chris Stoeckert, Jie Zheng + GROUP: ArrayExpress production team + DNA methylation profiling by high throughput sequencing design @@ -41656,10 +43495,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) biological activity assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|biological activity + A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|biological activity biological activity assay measuring epitope specific granzyme B release by T cells @@ -41671,21 +43510,37 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|ICS + A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -41697,21 +43552,37 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|ELISA + An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -41733,13 +43604,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -41748,12 +43619,12 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - all pairs design + all pairs design - A study design in which all specimens are compared to every other specimen. - Person: Chris Stoeckert, Jie Zheng - MO_565 all_pairs - all pairs design + A study design in which all specimens are compared to every other specimen. + Person: Chris Stoeckert, Jie Zheng + MO_565 all_pairs + all pairs design @@ -41770,10 +43641,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) proteomic profiling by array design - A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. - Person: Chris Stoeckert, Jie Zheng, Dan Berrios - Group: ArrayExpress production team - https://github.com/obi-ontology/obi/issues/854 + A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. + Person: Chris Stoeckert, Jie Zheng, Dan Berrios + Group: ArrayExpress production team + https://github.com/obi-ontology/obi/issues/854 proteomic profiling by array design @@ -41783,8 +43654,8 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - q-value - PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. + q-value + PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)" A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. @@ -41794,7 +43665,7 @@ To compute q-values, it is necessary to know the p-value produced by a test and Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - q-value + q-value @@ -41809,12 +43680,12 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - genotyping design + genotyping design - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. - Person: Chris Stoeckert, Jie Zheng - MO_560 genotyping_design - genotyping design + A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. + Person: Chris Stoeckert, Jie Zheng + MO_560 genotyping_design + genotyping design @@ -41822,25 +43693,40 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - + + + + - - + + + + + + + + + + + + + + + + + - - - - biological activity assay measuring epitope specific interleukin-2 production by T cells + + + + + assay measuring epitope specific interleukin-2 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|biological activity - biological activity assay measuring epitope specific interleukin-2 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|biological activity + assay measuring epitope specific interleukin-2 production by T cells @@ -41861,13 +43747,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific interleukin-15 production by T cells + epitope specific interleukin-15 production by T cells - A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-15 production by T cells + A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-15 production by T cells @@ -41888,13 +43774,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific macrophage inflammatory protein-1 gamma production by T cells + epitope specific macrophage inflammatory protein-1 gamma production by T cells - A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific macrophage inflammatory protein-1 gamma production by T cells + A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -41925,12 +43811,12 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - individual genetic characteristics comparison design + individual genetic characteristics comparison design - A study design where genotype, haplotype, or other individual genetic characteristics are compared. - Person: Chris Stoeckert, Jie Zheng - MO_527 individual_genetic_characteristics_design - individual genetic characteristics comparison design + A study design where genotype, haplotype, or other individual genetic characteristics are compared. + Person: Chris Stoeckert, Jie Zheng + MO_527 individual_genetic_characteristics_design + individual genetic characteristics comparison design @@ -41941,13 +43827,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -41955,13 +43851,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific interleukin-1 beta production by T cells + assay measuring epitope specific interleukin-1 beta production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|biological activity - biological activity assay measuring epitope specific interleukin-1 beta production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|biological activity + assay measuring epitope specific interleukin-1 beta production by T cells @@ -41972,13 +43868,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -41986,13 +43892,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific interleukin-4 production by T cells + assay measuring epitope specific interleukin-4 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|biological activity - biological activity assay measuring epitope specific interleukin-4 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|biological activity + assay measuring epitope specific interleukin-4 production by T cells @@ -42003,13 +43909,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -42017,13 +43933,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific interleukin-6 production by T cells + assay measuring epitope specific interleukin-6 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|biological activity - biological activity assay measuring epitope specific interleukin-6 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|biological activity + assay measuring epitope specific interleukin-6 production by T cells @@ -42034,21 +43950,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells - A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|bioassay + A reporter cell line analyte detection bioassay that detects tumor necrosis factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|bioassay cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells @@ -42060,10 +43992,25 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + @@ -42072,10 +44019,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells - An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - lymphotoxin A/TNFb release|ICS + A flow cytometry assay that detects lymphotoxin A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + lymphotoxin A/TNFb release|ICS intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells @@ -42091,12 +44038,12 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - pathogenicity design + pathogenicity design - A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. - Person: Chris Stoeckert, Jie Zheng - MO_807 pathogenicity_design - pathogenicity design + A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. + Person: Chris Stoeckert, Jie Zheng + MO_807 pathogenicity_design + pathogenicity design @@ -42107,21 +44054,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-5 production by T cells - An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-5 production by T cells @@ -42133,13 +44096,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -42147,13 +44120,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|biological activity - biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|biological activity + assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -42164,21 +44137,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-8 production by T cells - An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-8 release|cytometric bead array + A cytometric bead array assay that detects interleukin-8 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-8 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-8 production by T cells @@ -42190,13 +44179,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -42204,13 +44203,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|biological activity - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -42248,12 +44247,12 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - genetic modification design + genetic modification design - A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. - Person: Chris Stoeckert, Jie Zheng - MO_447 genetic_modification_design - genetic modification design + A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. + Person: Chris Stoeckert, Jie Zheng + MO_447 genetic_modification_design + genetic modification design @@ -42275,10 +44274,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html ELISA measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|ELISA + A T cell epitope specific granzyme B release assay that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|ELISA ELISA measuring epitope specific granzyme B release by T cells @@ -42300,13 +44299,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific IP-10 production by T cells + epitope specific IP-10 production by T cells - A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific IP-10 production by T cells + A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific IP-10 production by T cells @@ -42341,11 +44340,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html transcription profiling by array assay - A transcription profiling assay that uses array technology. - James Malone - RNA profiling by array assay - EFO:0002768 - https://sourceforge.net/p/obi/obi-terms/757/ + A transcription profiling assay that uses array technology. + James Malone + RNA profiling by array assay + EFO:0002768 + https://sourceforge.net/p/obi/obi-terms/757/ transcription profiling by array assay @@ -42377,12 +44376,12 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - strain comparison design + strain comparison design - A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. - Person: Chris Stoeckert, Jie Zheng - MO_462 strain_or_line_design - strain comparison design + A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. + Person: Chris Stoeckert, Jie Zheng + MO_462 strain_or_line_design + strain comparison design @@ -42393,13 +44392,23 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + @@ -42407,13 +44416,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells + assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|biological activity - biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells + A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|biological activity + assay measuring epitope specific monocyte chemotactic protein-1 production by T cells @@ -42424,21 +44433,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells - An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ICS + A flow cytometry assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells @@ -42461,10 +44486,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html in vivo assay measuring T cell epitope specific disease exacerbation - An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. - IEDB - IEDB - disease exacerbation|in vivo assay + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. + IEDB + IEDB + disease exacerbation|in vivo assay in vivo assay measuring T cell epitope specific disease exacerbation @@ -42488,10 +44513,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html cell specimen - A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. + A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ - PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl - MO_612 cell + PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl + MO_612 cell cell specimen @@ -42509,10 +44534,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html monospecific T cell recognition assay measuring MHC ligand processing and presentation - A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - ligand presentation|T cell recognition + A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + ligand presentation|T cell recognition monospecific T cell recognition assay measuring MHC ligand processing and presentation @@ -42534,13 +44559,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific interleukin-17F production by T cells + epitope specific interleukin-17F production by T cells - A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-17F production by T cells + A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-17F production by T cells @@ -42549,13 +44574,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - T cell epitope specific immune intervention - Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide + T cell epitope specific immune intervention + Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide - An epitope specific immune intervention in which the induced response targets a T cell epitope - PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - T cell epitope specific immune intervention + An epitope specific immune intervention in which the induced response targets a T cell epitope + PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + T cell epitope specific immune intervention @@ -42582,9 +44607,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html specimen with known storage state - A specimen for which it is known whether it has been subjected to storage of a specified type. - PERSON: Chris Stoeckert, Jie Zheng - MO_95 BiosourceType + A specimen for which it is known whether it has been subjected to storage of a specified type. + PERSON: Chris Stoeckert, Jie Zheng + MO_95 BiosourceType specimen with known storage state @@ -42611,10 +44636,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html in vivo assay measuring T cell epitope specific protection from tumor challenge - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. - IEDB - IEDB - tumor burden after challenge|in vivo assay + A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. + IEDB + IEDB + tumor burden after challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from tumor challenge @@ -42626,9 +44651,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html lowess group transformation - A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. - Person: Elisabetta Manduchi - MO_861 lowess_group_normalization + A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. + Person: Elisabetta Manduchi + MO_861 lowess_group_normalization lowess group transformation @@ -42665,10 +44690,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. - IEDB - IEDB - pathogen burden after challenge|in vivo assay + A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. + IEDB + IEDB + pathogen burden after challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden @@ -42698,11 +44723,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html phage display binding assay - Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. + Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. - A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. - IEDB - IEDB + A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. + IEDB + IEDB phage display binding assay @@ -42720,9 +44745,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html lowess transformation - A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. - Person: Elisabetta Manduchi - MO_720 lowess_normalization + A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. + Person: Elisabetta Manduchi + MO_720 lowess_normalization lowess transformation @@ -42745,10 +44770,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html mass spectrometry assay measuring MHC ligand processing and presentation - A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands - IEDB - IEDB - ligand presentation|mass spectrometry + A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands + IEDB + IEDB + ligand presentation|mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation @@ -42781,10 +44806,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html specimen from organism - A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). - PERSON: Chris Stoeckert, Jie Zheng + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + PERSON: Chris Stoeckert, Jie Zheng tissue specimen - MO_954 organism_part + MO_954 organism_part specimen from organism @@ -42800,14 +44825,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - phage display library panning - Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind. + phage display library panning + Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind. - Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. + Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. - Jason Greenbaum, Randi Vita, Bjoern Peters - IEDB, http://en.wikipedia.org/wiki/Phage_display - phage display library panning + Jason Greenbaum, Randi Vita, Bjoern Peters + IEDB, http://en.wikipedia.org/wiki/Phage_display + phage display library panning @@ -42818,9 +44843,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html lowess global transformation - A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. - Person: Elisabetta Manduchi - MO_692 lowess_global_normalization + A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. + Person: Elisabetta Manduchi + MO_692 lowess_global_normalization lowess global transformation @@ -42832,21 +44857,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells - An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - TGFb release|ICS + A flow cytometry assay that detects transforming growth factor-beta production by T cells. + IEDB + IEDB + TGFb release|ICS intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells @@ -42886,9 +44927,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html cell collecting - A planned process that collects cells from culture. - PERSON: Chris Stoeckert, Jie Zheng - MO_982 harvest + A planned process that collects cells from culture. + PERSON: Chris Stoeckert, Jie Zheng + MO_982 harvest cell collecting @@ -42911,10 +44952,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html biological activity assay measuring T cell epitope specific in vivo activity - A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. - IEDB - IEDB - in vivo activity|biological activity + A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. + IEDB + IEDB + in vivo activity|biological activity biological activity assay measuring T cell epitope specific in vivo activity @@ -42938,13 +44979,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - purified MHC molecule preparation - HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody + purified MHC molecule preparation + HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody - A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. - BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general. - Bjoern Peters - purified MHC molecule preparation + A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. + BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general. + Bjoern Peters + purified MHC molecule preparation @@ -42959,13 +45000,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - disposition to be bound by an MHC protein complex + disposition to be bound by an MHC protein complex - Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. - PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters - MHC ligand disposition - IEDB - disposition to be bound by an MHC protein complex + Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. + PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters + MHC ligand disposition + IEDB + disposition to be bound by an MHC protein complex @@ -42974,13 +45015,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - B cell epitope specific immune intervention - Injecting a mouse with recombinant antibody targeting an anthrax epitope + B cell epitope specific immune intervention + Injecting a mouse with recombinant antibody targeting an anthrax epitope - An epitope specific immune intervention in which the induced response targets a B cell epitope - PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - B cell epitope specific immune intervention + An epitope specific immune intervention in which the induced response targets a B cell epitope + PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + B cell epitope specific immune intervention @@ -42991,10 +45032,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html epitope tolerance induction experiment - An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response - IEDB - tolerance induction - IEDB + An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response + IEDB + tolerance induction + IEDB epitope tolerance induction experiment @@ -43012,10 +45053,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC - A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. - IEDB - IEDB - ligand presentation|cellular MHC/mass spectrometry + A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. + IEDB + IEDB + ligand presentation|cellular MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC @@ -43027,21 +45068,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|cytometric bead array + A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|cytometric bead array cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -43059,10 +45116,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html radioactivity detection binding assay - A binding assay that uses radioactivity detection as an indicator of binding. - Bjoern Peters - Randi Vita - IEDB + A binding assay that uses radioactivity detection as an indicator of binding. + Bjoern Peters + Randi Vita + IEDB radioactivity detection binding assay @@ -43085,10 +45142,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html in vivo assay measuring T cell epitope specific protection based on survival - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. - IEDB - IEDB - survival from challenge|in vivo assay + A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. + IEDB + IEDB + survival from challenge|in vivo assay in vivo assay measuring T cell epitope specific protection based on survival @@ -43136,12 +45193,29 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + + + + + + + + + + + + + + + + + cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition - A cell bound MHC binding assay that uses a T cell epitope recognition assay. - IEDB - IEDB - qualitative binding|cellular MHC/T cell inhibition + A cell bound MHC binding assay that uses a T cell epitope recognition assay. + IEDB + IEDB + qualitative binding|cellular MHC/T cell inhibition cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition @@ -43152,11 +45226,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html linear amplification - An example is the use of the T7 promoter for amplification by transcribing many RNA copies. + An example is the use of the T7 promoter for amplification by transcribing many RNA copies. - An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. - PERSON: Chris Stoeckert, Jie Zheng - MO_997 linear_amplification + An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. + PERSON: Chris Stoeckert, Jie Zheng + MO_997 linear_amplification linear amplification @@ -43184,10 +45258,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html biological activity assay measuring epitope specific T cell helper activity - A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. - IEDB - IEDB - helper response|biological activity + A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. + IEDB + IEDB + helper response|biological activity biological activity assay measuring epitope specific T cell helper activity @@ -43199,21 +45273,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells - An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - IL-22 release|ICS + A flow cytometry assay that detects interleukin-22 production by T cells. + IEDB + IEDB + IL-22 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells @@ -43241,10 +45331,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html biological activity assay measuring epitope specific perforin release by T cells - A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. - IEDB - IEDB - perforin release|biological activity + A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. + IEDB + IEDB + perforin release|biological activity biological activity assay measuring epitope specific perforin release by T cells @@ -43256,9 +45346,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html atmosphere - A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. - PERSON: Chris Stoeckert, Jie Zheng - MO_219 atmosphere + A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. + PERSON: Chris Stoeckert, Jie Zheng + MO_219 atmosphere atmosphere @@ -43276,10 +45366,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html fluorescence detection binding assay - A binding assay that uses fluorescence detection as an indicator of binding - Bjoern Peters - Randi Vita - IEDB + A binding assay that uses fluorescence detection as an indicator of binding + Bjoern Peters + Randi Vita + IEDB fluorescence detection binding assay @@ -43313,10 +45403,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand - A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - ligand presentation|coelution + A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + ligand presentation|coelution coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand @@ -43348,11 +45438,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html fluorescence detection assay - Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. + Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. - An assay in which a material's fluorescence is determined. - IEDB - IEDB + An assay in which a material's fluorescence is determined. + IEDB + IEDB fluorescence detection assay @@ -43373,12 +45463,12 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific perforin production by T cells + epitope specific perforin production by T cells - The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. - Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation - PERSON: Bjoern Peters, Randi Vita - epitope specific perforin production by T cells + The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. + Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation + PERSON: Bjoern Peters, Randi Vita + epitope specific perforin production by T cells @@ -43418,14 +45508,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - MHC protein complex binding to ligand - The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. + MHC protein complex binding to ligand + The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. - The process in which a ligand binds to an MHC molecule to form a stable complex - 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. - PERSON: Bjoern Peters; Randi Vita - IEDB - MHC protein complex binding to ligand + The process in which a ligand binds to an MHC molecule to form a stable complex + 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. + PERSON: Bjoern Peters; Randi Vita + IEDB + MHC protein complex binding to ligand @@ -43442,10 +45532,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html dissection - A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. - PERSON: Chris Stoeckert, Jie Zheng - EFO_0003856 dissection - MO_374 dissect + A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. + PERSON: Chris Stoeckert, Jie Zheng + EFO_0003856 dissection + MO_374 dissect dissection @@ -43463,9 +45553,9 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html purification - A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest - PERSON: Chris Stoeckert, Jie Zheng - MO_406 purify + A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest + PERSON: Chris Stoeckert, Jie Zheng + MO_406 purify purification @@ -43510,10 +45600,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html specimen with pre- or post-mortem status - A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. - organizational term, used in description of specimen that is created from known pre- or post-mortem status - PERSON: Chris Stoeckert, Jie Zheng - MO_84 OrganismStatus + A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. + organizational term, used in description of specimen that is created from known pre- or post-mortem status + PERSON: Chris Stoeckert, Jie Zheng + MO_84 OrganismStatus specimen with pre- or post-mortem status @@ -43536,10 +45626,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html in vivo assay measuring T cell epitope specific treatment of disease - An efficacy of T cell epitope intervention experiment that detects a decrease in disease. - IEDB - IEDB - decreased disease|in vivo assay + An efficacy of T cell epitope intervention experiment that detects a decrease in disease. + IEDB + IEDB + decreased disease|in vivo assay in vivo assay measuring T cell epitope specific treatment of disease @@ -43551,7 +45641,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html sampling time measurement datum - A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. + A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint @@ -43577,10 +45667,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html Edman degradation assay measuring MHC ligand processing and presentation - A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - ligand presentation|Edman degradation + A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + ligand presentation|Edman degradation Edman degradation assay measuring MHC ligand processing and presentation @@ -43598,10 +45688,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC - A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. - IEDB - IEDB - ligand presentation|secreted MHC/mass spectrometry + A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. + IEDB + IEDB + ligand presentation|secreted MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC @@ -43617,13 +45707,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - disposition to be a product of antigen processing and presentation - The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. + disposition to be a product of antigen processing and presentation + The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. - A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. - IEDB - IEDB - disposition to be a product of antigen processing and presentation + A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. + IEDB + IEDB + disposition to be a product of antigen processing and presentation @@ -43634,10 +45724,25 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + @@ -43646,10 +45751,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html cytometric bead array assay measuring epitope specific interleukin-17A production by T cells - A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay. - IEDB - IEDB - IL-17A release|cytometric bead array + A cytometric bead array assay that detects interleukin-17A production by T cells. + IEDB + IEDB + IL-17A release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17A production by T cells @@ -43658,13 +45763,8 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + - - - - - - @@ -43697,13 +45797,30 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex - A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC/competitive/radioactivity - purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC/competitive/radioactivity + radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex @@ -43724,13 +45841,13 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - minimal inhibitory concentration + minimal inhibitory concentration - A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. - Created following request by Albert Goldfain - PERSON:Bjoern Peters - Bjoern Peters, coordinated with Albert Goldfain - minimal inhibitory concentration + A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. + Created following request by Albert Goldfain + PERSON:Bjoern Peters + Bjoern Peters, coordinated with Albert Goldfain + minimal inhibitory concentration @@ -43750,15 +45867,15 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - material maintenance service - model organism colony maintanance + material maintenance service + model organism colony maintanance - A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. - material maintenance service + A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. + material maintenance service @@ -43769,11 +45886,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - + @@ -43788,6 +45901,19 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + + + + + + + + + + + + + @@ -43800,14 +45926,15 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + - cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex - A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM - cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM + radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex @@ -43818,11 +45945,157 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex + + A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex + + + + + + + + + + + + + + + + + + + + + epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + + A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex + + A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|lysate MHC/direct/fluorescence + fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex + + + + + + + + + + + @@ -43853,129 +46126,15 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - + - - - - - cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection - - A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM - cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection - - - - - - - - - - - - - - - - - - - - epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - - A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - - - - - - - - - - - - - - - - - - - - - + + - - + + - - - - - - cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection - - A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|lysate MHC/direct/fluorescence - cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -43990,14 +46149,15 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + - cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM - cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -44008,21 +46168,37 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells - An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA. - IEDB - IEDB - G-CSF release|ELISA + An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. + IEDB + IEDB + G-CSF release|ELISA ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells @@ -44050,10 +46226,25 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - - + + + + + + + + + + + + + + + + + @@ -44062,10 +46253,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html cytometric bead array assay measuring epitope specific interleukin-17F production by T cells - A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay. - IEDB - IEDB - IL-17F release|cytometric bead array + A cytometric bead array assay that detects interleukin-17F production by T cells. + IEDB + IEDB + IL-17F release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17F production by T cells @@ -44077,11 +46268,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - + @@ -44096,6 +46283,19 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + + + + + + + + + + + + + @@ -44108,14 +46308,15 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + - cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding. - IEDB - IEDB - association constant KA|cellular MHC/direct/fluorescence|1/M - cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand. + IEDB + IEDB + association constant KA|cellular MHC/direct/fluorescence|1/M + fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex @@ -44124,14 +46325,14 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - PDB file - The file found in the pdb with the identifier 3pe4 + PDB file + The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 - A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. - PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum - PDB file + A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. + PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum + PDB file @@ -44152,13 +46353,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - epitope specific interleukin-17A production by T cells + epitope specific interleukin-17A production by T cells - A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific interleukin-17A production by T cells + A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific interleukin-17A production by T cells @@ -44167,14 +46368,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - support service - An help desk for an instrument or a software. + support service + An help desk for an instrument or a software. - A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON; Carlo Torniai - support service + A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON; Carlo Torniai + support service @@ -44207,14 +46408,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - material service - A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization + material service + A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization - A service which has a material entity as specified input and/or specified output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material service + A service which has a material entity as specified input and/or specified output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material service @@ -44229,14 +46430,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - data analysis service - Statistaical analysis service, data visualization service + data analysis service + Statistaical analysis service, data visualization service - A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - data analysis service + A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + data analysis service @@ -44257,15 +46458,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - data service - Data analysis service such statistical abalysis or storage service such data backup. + data service + Data analysis service such statistical abalysis or storage service such data backup. - A service that has some information content entity as input and output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - Information content entity was used as specified input and output since it was more appropriate then data item or dataset. - data service + A service that has some information content entity as input and output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + Information content entity was used as specified input and output since it was more appropriate then data item or dataset. + data service @@ -44276,11 +46477,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -44295,6 +46492,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -44307,14 +46517,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex - A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. - IEDB - IEDB - half life|purified MHC/direct/fluorescence|min - purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + half life|purified MHC/direct/fluorescence|min + fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex @@ -44325,21 +46536,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-9 production by T cells - An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-9 release|cytometric bead array + A cytometric bead array assay that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-9 production by T cells @@ -44349,14 +46576,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - data storage service - A service offering data backup + data storage service + A service offering data backup - A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - data storage service + A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + data storage service @@ -44364,13 +46591,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -44403,13 +46625,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection + + + + + + + + + + + + + + + + + + fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex - A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - IEDB - IEDB - qualitative binding|purified MHC/competitive/fluorescence - purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + IEDB + IEDB + qualitative binding|purified MHC/competitive/fluorescence + fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex @@ -44430,13 +46669,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - epitope specific interleukin-7 production by T cells + epitope specific interleukin-7 production by T cells - A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific interleukin-7 production by T cells + A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific interleukin-7 production by T cells @@ -44451,13 +46690,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - equilibrium dissociation constant (KD) - KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb + equilibrium dissociation constant (KD) + KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb - A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) - PERSON: Bjoern Peters, Randi Vita - IEDB - equilibrium dissociation constant (KD) + A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) + PERSON: Bjoern Peters, Randi Vita + IEDB + equilibrium dissociation constant (KD) @@ -44468,11 +46707,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -44501,6 +46736,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -44513,14 +46761,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|purified MHC/competitive/fluorescence|nM - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|purified MHC/competitive/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex @@ -44535,14 +46784,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - training service - A service that offers training for a specific instrument or technique. A course to learn how to use a microscope + training service + A service that offers training for a specific instrument or technique. A course to learn how to use a microscope - A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - training service + A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + training service @@ -44553,11 +46802,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -44586,6 +46831,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -44598,14 +46856,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - IEDB - IEDB - dissociation constant KD|cellular MHC/competitive/fluorescence|nM - cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + IEDB + IEDB + dissociation constant KD|cellular MHC/competitive/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -44615,14 +46874,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete T cell recognition of eluted MHC ligand assay - Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. + Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. - An assay that identifies an MHC ligand using a T cell response assay as a readout - PERSON: Randi Vita, Bjoern Peters - IEDB + An assay that identifies an MHC ligand using a T cell response assay as a readout + PERSON: Randi Vita, Bjoern Peters + IEDB - T cell recognition + T cell recognition obsolete T cell recognition of eluted MHC ligand assay true @@ -44635,11 +46894,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -44654,6 +46909,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -44666,14 +46934,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex - A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. - IEDB - IEDB - on rate|purified MHC/direct/fluorescence|nM^-1s^-1 - purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex. + IEDB + IEDB + on rate|purified MHC/direct/fluorescence|nM^-1s^-1 + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex @@ -44684,21 +46953,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells - An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - IL-13 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells. + IEDB + IEDB + IL-13 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells @@ -44707,47 +46992,58 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - + + - - + + + + + + + - - - - purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection + + + + + + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 - A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. - IEDB - IEDB - dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM - purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. + IEDB + IEDB + dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 @@ -44758,11 +47054,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -44791,6 +47083,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -44803,14 +47108,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex - A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|lysate MHC/competitive/radioactivity|nM - cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|lysate MHC/competitive/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex @@ -44821,21 +47127,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - CCL3/MIP-1a release|ICS + A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. + IEDB + IEDB + CCL3/MIP-1a release|ICS intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -44913,13 +47235,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - comparative phenotypic assessment + comparative phenotypic assessment - Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference - Philly workshop 2011 - Philly workshop 2011 - 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 - comparative phenotypic assessment + Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference + Philly workshop 2011 + Philly workshop 2011 + 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 + comparative phenotypic assessment @@ -44939,14 +47261,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - material analysis service - Services performing DNA sequencing or Cell Analysis + material analysis service + Services performing DNA sequencing or Cell Analysis - A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - material analysis service + A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + material analysis service @@ -44955,13 +47277,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - equilibrium association constant (KA) - KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. + equilibrium association constant (KA) + KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. - A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) - PERSON: Bjoern Peters, Randi Vita - IEDB - equilibrium association constant (KA) + A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) + PERSON: Bjoern Peters, Randi Vita + IEDB + equilibrium association constant (KA) @@ -44972,11 +47294,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45005,6 +47323,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45017,14 +47348,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|cellular MHC/competitive/radioactivity|nM - cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|cellular MHC/competitive/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex @@ -45035,7 +47367,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -45050,17 +47382,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + - cell bound MHC binding assay measuring binding of a MHC:ligand complex + assay measuring binding of a cell-bound-MHC:ligand complex - A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC - cell bound MHC binding assay measuring binding of a MHC:ligand complex + A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC + assay measuring binding of a cell-bound-MHC:ligand complex @@ -45069,15 +47414,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - access service - A service that provides acess to a mass spectrometer. + access service + A service that provides acess to a mass spectrometer. - A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. - Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - access service + A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. + Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + access service @@ -45088,10 +47433,25 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + @@ -45100,10 +47460,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFSF11/RANKL release|ICS + A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFSF11/RANKL release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells @@ -45115,21 +47475,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + + + + + + + + + + - + assay measuring a binding constant of a MHC:ligand complex - A MHC:ligand binding assay that measures a binding constant. - IEDB - IEDB - binding constant|binding assay + A MHC:ligand binding assay that measures a binding constant. + IEDB + IEDB + binding constant|binding assay assay measuring a binding constant of a MHC:ligand complex @@ -45139,13 +47508,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - rate measurement datum - The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. + rate measurement datum + The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. - A scalar measurement datum that represents the number of events occuring over a time interval - PERSON: Bjoern Peters, Randi Vita - IEDB - rate measurement datum + A scalar measurement datum that represents the number of events occuring over a time interval + PERSON: Bjoern Peters, Randi Vita + IEDB + rate measurement datum @@ -45156,7 +47525,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -45171,17 +47540,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + - purified MHC binding assay measuring binding of a MHC:ligand complex + assay measuring binding of a purified-MHC:ligand complex - A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC - purified MHC binding assay measuring binding of a MHC:ligand complex + A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC + assay measuring binding of a purified-MHC:ligand complex @@ -45189,36 +47571,49 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection + + + + + + + + radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex - A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|lysate MHC/direct/radioactivity - cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|lysate MHC/direct/radioactivity + radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex @@ -45238,14 +47633,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - material storage service - A service that offers liquid nitrogen stroage. + material storage service + A service that offers liquid nitrogen stroage. - A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - material storage service + A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + material storage service @@ -45256,11 +47651,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45275,6 +47666,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45287,14 +47691,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. - IEDB - IEDB - half life|cellular MHC/direct/radioactivity|min - cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. + IEDB + IEDB + half life|cellular MHC/direct/radioactivity|min + radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex @@ -45305,11 +47710,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45324,6 +47725,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45336,14 +47750,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half life|cellular MHC/direct/fluorescence|min - cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half life|cellular MHC/direct/fluorescence|min + fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex @@ -45354,9 +47769,9 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete cell lysate MHC binding constant determination assay - An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. - PERSON: Bjoern Peters - IEDB + An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. + PERSON: Bjoern Peters + IEDB obsolete cell lysate MHC binding constant determination assay true @@ -45370,11 +47785,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45389,6 +47800,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45401,14 +47825,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. - IEDB - IEDB - half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM - cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand. + IEDB + IEDB + half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex @@ -45419,10 +47844,25 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + @@ -45431,10 +47871,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells - A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay. - IEDB - IEDB - IL-17F release|ICS + A flow cytometry assay that detects interleukin-17F production by T cells. + IEDB + IEDB + IL-17F release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells @@ -45450,14 +47890,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - material processing service - A service for cell line creation. A service providing cel line immortalization. + material processing service + A service for cell line creation. A service providing cel line immortalization. - A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material processing service + A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material processing service @@ -45465,63 +47905,72 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - + + + + + - - + + - - - - - - - - - - - - + - - - - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection + + + + + + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. - IEDB - IEDB - dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. + IEDB + IEDB + dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 @@ -45532,11 +47981,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45551,6 +47996,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45563,14 +48021,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex - A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half life|lysate MHC/direct/radioactivity|min - cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half life|lysate MHC/direct/radioactivity|min + radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex @@ -45578,23 +48037,22 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - 50% dissociation of binding temperature (Tm) - Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. + 50% dissociation of binding temperature (Tm) + Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. - A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. - - PERSON: Bjoern Peters, Randi Vita - melting temperature (Tm) - IEDB - 50% dissociation of binding temperature (Tm) + A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. + PERSON: Bjoern Peters, Randi Vita + melting temperature (Tm) + IEDB + 50% dissociation of binding temperature (Tm) @@ -45605,11 +48063,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45624,6 +48078,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45636,14 +48103,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex - A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|lysate MHC/direct/radioactivity|1/s - cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|lysate MHC/direct/radioactivity|1/s + radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex @@ -45654,11 +48122,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45687,6 +48151,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45699,14 +48176,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex - A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM - purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex @@ -45717,11 +48195,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -45736,6 +48210,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -45748,14 +48235,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex - A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. - IEDB - IEDB - off rate|purified MHC/direct/fluorescence|1/s - purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + off rate|purified MHC/direct/fluorescence|1/s + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex @@ -45766,13 +48254,23 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + + + + + + + + + + + @@ -45780,13 +48278,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells + assay measuring epitope specific vascular endothelial growth factor production by T cells - A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|biological activity - biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells + A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|biological activity + assay measuring epitope specific vascular endothelial growth factor production by T cells @@ -45794,15 +48292,31 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - equilibrium dissociation constant (KD) approximated by IC50 + + + + + + + + + + + + + + + + + + + equilibrium dissociation constant (KD) approximated by IC50 - A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. - PERSON: Bjoern Peters, Randi Vita - http://dx.doi.org/10.1016/0006-2952(73)90196-2 + A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. + PERSON: Bjoern Peters, Randi Vita + http://dx.doi.org/10.1016/0006-2952(73)90196-2 - equilibrium dissociation constant (KD) approximated by IC50 + equilibrium dissociation constant (KD) approximated by IC50 @@ -45813,9 +48327,9 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete cell bound MHC binding constant determination assay - An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. - PERSON: Bjoern Peters - IEDB + An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. + PERSON: Bjoern Peters + IEDB obsolete cell bound MHC binding constant determination assay true @@ -45833,14 +48347,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - DNA sequence data - The part of a FASTA file that contains the letters ACTGGGAA + DNA sequence data + The part of a FASTA file that contains the letters ACTGGGAA - A sequence data item that is about the primary structure of DNA - OBI call; Bjoern Peters - OBI call; Melanie Courtout - 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. - DNA sequence data + A sequence data item that is about the primary structure of DNA + OBI call; Bjoern Peters + OBI call; Melanie Courtout + 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. + DNA sequence data @@ -45851,12 +48365,12 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete cell lysate MHC competitive binding assay using radioactivity detection - competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - cell lysate MHC competitive binding using radioactivity + cell lysate MHC competitive binding using radioactivity obsolete cell lysate MHC competitive binding assay using radioactivity detection true @@ -45878,12 +48392,12 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - assigning gene property based on phenotypic assessment + assigning gene property based on phenotypic assessment - Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. - Philly workshop 2011 - Philly workshop 2011 - assigning gene property based on phenotypic assessment + Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. + Philly workshop 2011 + Philly workshop 2011 + assigning gene property based on phenotypic assessment @@ -45894,9 +48408,9 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete purified MHC binding constant determination assay - An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. - PERSON: Bjoern Peters - IEDB + An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. + PERSON: Bjoern Peters + IEDB obsolete purified MHC binding constant determination assay true @@ -45910,21 +48424,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells - An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-22 release|cytometric bead array + A cytometric bead array assay that detects interleukin-22 production by T cells. + IEDB + IEDB + IL-22 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells @@ -45936,21 +48466,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific vascular endothelial growth factor production by T cells - An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA. - IEDB - IEDB - VEGF release|ELISA + An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|ELISA ELISA measuring epitope specific vascular endothelial growth factor production by T cells @@ -45962,7 +48508,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -45977,17 +48523,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + - cell lysate MHC binding assay measuring binding of a MHC:ligand complex + assay measuring binding of a cell-lysate-MHC:ligand complex - A MHC binding qualitative binding to ligand assay using MHC in a cell lysate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|lysate MHC - cell lysate MHC binding assay measuring binding of a MHC:ligand complex + A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|lysate MHC + assay measuring binding of a cell-lysate-MHC:ligand complex @@ -45996,14 +48555,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - material transport service - A service for chemical disposal + material transport service + A service for chemical disposal - A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material transport service + A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material transport service @@ -46011,14 +48570,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - equilibrium dissociation constant (KD) approximated by EC50 + + + + + + + + + + + + + + + + + + + equilibrium dissociation constant (KD) approximated by EC50 - A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. - PERSON: Bjoern Peters, Randi Vita - Assay Development: Fundamentals and Practices, By Ge Wu, page 74 - equilibrium dissociation constant (KD) approximated by EC50 + A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. + PERSON: Bjoern Peters, Randi Vita + Assay Development: Fundamentals and Practices, By Ge Wu, page 74 + equilibrium dissociation constant (KD) approximated by EC50 @@ -46029,11 +48604,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete cell bound MHC direct binding assay - direct binding assay measuring MHC ligand binding using MHC derived from a cell - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + direct binding assay measuring MHC ligand binding using MHC derived from a cell + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - cell bound MHC direct binding + cell bound MHC direct binding obsolete cell bound MHC direct binding assay true @@ -46043,15 +48618,31 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + + + + - half life of binding datum - The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. + half life of binding datum + The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. - A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. - PERSON: Bjoern Peters, Randi Vita - IEDB - half life of binding datum + A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. + PERSON: Bjoern Peters, Randi Vita + IEDB + half life of binding datum @@ -46059,36 +48650,49 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display + + + + + + + + phage display binding assay measuring binding of a purified-MHC:ligand complex - A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC/direct/phage display - purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display + A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC/direct/phage display + phage display binding assay measuring binding of a purified-MHC:ligand complex @@ -46099,21 +48703,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-7 production by T cells - An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-7 release|cytometric bead array + A cytometric bead array assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-7 production by T cells @@ -46125,11 +48745,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -46144,6 +48760,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -46156,14 +48785,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex - A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half life|purified MHC/direct/radioactivity|min - purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half life|purified MHC/direct/radioactivity|min + radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex @@ -46174,13 +48804,23 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + + + + + + + + + + + @@ -46188,13 +48828,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - biological activity assay measuring epitope specific interleukin-7 production by T cells + assay measuring epitope specific interleukin-7 production by T cells - A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. - IEDB - IEDB - IL-7 release|biological activity - biological activity assay measuring epitope specific interleukin-7 production by T cells + A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|biological activity + assay measuring epitope specific interleukin-7 production by T cells @@ -46203,14 +48843,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - binding - A peptide binding to an MHC molecule to form a complex. + binding + A peptide binding to an MHC molecule to form a complex. - The process of material entities forming complexes. - 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. - PERSON: Bjoern Peters, Randi Vita - IEDB - binding + The process of material entities forming complexes. + 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. + PERSON: Bjoern Peters, Randi Vita + IEDB + binding @@ -46221,10 +48861,25 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + @@ -46233,10 +48888,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells - A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay. - IEDB - IEDB - IL-17A release|ICS + A flow cytometry assay that detects interleukin-17A production by T cells. + IEDB + IEDB + IL-17A release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells @@ -46245,13 +48900,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -46268,13 +48918,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection + + + + + + + + + + + + + + + + + + fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex - A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC/direct/fluorescence - purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC/direct/fluorescence + fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex @@ -46284,12 +48951,12 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N direct binding assay - Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ + Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ - A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. - Bjoern Peters - Randi Vita - IEDB + A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. + Bjoern Peters + Randi Vita + IEDB direct binding assay @@ -46301,11 +48968,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -46320,6 +48983,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -46332,14 +49008,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex - A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding. - IEDB - IEDB - half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM - purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex @@ -46365,11 +49042,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N competitive inhibition of binding assay - Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ + Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ - A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. - IEDB - IEDB + A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. + IEDB + IEDB competitive inhibition of binding assay @@ -46378,13 +49055,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -46417,13 +49089,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection + + + + + + + + + + + + + + + + + + fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC/competitive/fluorescence - cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC/competitive/fluorescence + fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex @@ -46434,11 +49123,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -46457,6 +49142,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + @@ -46469,13 +49163,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + X-ray crystallography assay determining the 3D structure of a MHC:ligand complex - A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|x-ray crystallography|angstroms + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a MHC:ligand complex @@ -46491,13 +49186,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - PDB file chain - The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex + PDB file chain + The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex - A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities - PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum - IEDB - PDB file chain + A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities + PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum + IEDB + PDB file chain @@ -46541,6 +49236,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -46556,10 +49264,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition - A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. - IEDB - IEDB - half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM + A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. + IEDB + IEDB + half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition @@ -46569,14 +49277,14 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - data maintenance service - A database management service, a web hosting service. + data maintenance service + A database management service, a web hosting service. - A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - data maintenance service + A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + data maintenance service @@ -46584,13 +49292,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -46623,13 +49326,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - IEDB - IEDB - qualitative binding|cellular MHC/competitive/radioactivity - cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + IEDB + IEDB + qualitative binding|cellular MHC/competitive/radioactivity + radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex @@ -46640,13 +49360,23 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + + + + + + + + + + + @@ -46654,13 +49384,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells + assay measuring epitope specific granulocyte colony stimulating factor production by T cells - A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. - IEDB - IEDB - G-CSF release|biological activity - biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells + A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. + IEDB + IEDB + G-CSF release|biological activity + assay measuring epitope specific granulocyte colony stimulating factor production by T cells @@ -46671,21 +49401,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells - An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-21 release|cytometric bead array + A cytometric bead array assay that detects interleukin-21 production by T cells. + IEDB + IEDB + IL-21 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells @@ -46694,13 +49440,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -46717,13 +49458,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC binding assay that uses radioactivity detection to detect direct binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC/direct/radioactivity - cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC/direct/radioactivity + radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex @@ -46733,12 +49491,28 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - binding off rate measurement datum (koff) + + + + + + + + + + + + + + + + + binding off rate measurement datum (koff) - A rate measurement datum of how quickly bound complexes disassociate - PERSON: Bjoern Peters, Randi Vita - IEDB - binding off rate measurement datum (koff) + A rate measurement datum of how quickly bound complexes disassociate + PERSON: Bjoern Peters, Randi Vita + IEDB + binding off rate measurement datum (koff) @@ -46746,53 +49520,58 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - + + - - + + + + + + + - - - - purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection + + + + + + fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex - A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 50% dissociation temperature|purified MHC/direct/fluorescence|°C - purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 50% dissociation temperature|purified MHC/direct/fluorescence|°C + fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex @@ -46802,12 +49581,28 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - binding on rate measurement datum (kon) + + + + + + + + + + + + + + + + + binding on rate measurement datum (kon) - A rate measurement datum of how quickly bound complexes form - PERSON: Bjoern Peters, Randi Vita - IEDB - binding on rate measurement datum (kon) + A rate measurement datum of how quickly bound complexes form + PERSON: Bjoern Peters, Randi Vita + IEDB + binding on rate measurement datum (kon) @@ -46815,13 +49610,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -46838,13 +49628,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection + + + + + + + + + + + + + + + + + + fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC binding assay that uses fluorescence detection to detect direct binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC/direct/fluorescence - cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC/direct/fluorescence + fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex @@ -46855,13 +49662,23 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + + + + + + + + + + + @@ -46869,13 +49686,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. - IEDB - IEDB - TNFSF11/RANKL release|biological activity - biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. + IEDB + IEDB + TNFSF11/RANKL release|biological activity + assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells @@ -46883,13 +49700,8 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - - - - - - @@ -46906,13 +49718,30 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex - A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding. - IEDB - IEDB - qualitative binding|purified MHC/direct/radioactivity - purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + qualitative binding|purified MHC/direct/radioactivity + radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex @@ -46923,21 +49752,37 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells - An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - IL-8 release|ICS + A flow cytometry assay that detects interleukin-8 production by T cells. + IEDB + IEDB + IL-8 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells @@ -46949,22 +49794,38 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - - + + + + + + + + + + + + + + + + + - cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells + + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells - An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-23 release|cytometric bead array - cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells + A cytometric bead array assay that detects interleukin-23 production by T cells. + IEDB + IEDB + IL-23 release|cytometric bead array + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells @@ -46975,11 +49836,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N obsolete purified MHC direct binding assay - direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - purified MHC direct binding + purified MHC direct binding obsolete purified MHC direct binding assay true @@ -47002,13 +49863,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - epitope specific vascular endothelial growth factor production by T cells + epitope specific vascular endothelial growth factor production by T cells - A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific vascular endothelial growth factor production by T cells + A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific vascular endothelial growth factor production by T cells @@ -47019,11 +49880,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - + @@ -47052,6 +49909,19 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + + + + + + + + + + + + + @@ -47064,14 +49934,15 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N + - purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex - A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM - purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex @@ -47113,7 +49984,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group - study description + study description project description NIAID GSCID-BRC investigation description @@ -47268,7 +50139,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N A textual entity that denotes an investigation. Person:Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group - study title + study title project title NIAID GSCID-BRC investigation title @@ -47329,10 +50200,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N organism identification assay - An assay that identifies the organism species in a specimen. - Chris Stoeckert - Jie Zheng - NIAID GSCID-BRC metadata working group + An assay that identifies the organism species in a specimen. + Chris Stoeckert + Jie Zheng + NIAID GSCID-BRC metadata working group organism identification assay @@ -47493,11 +50364,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N analytical chromatography - Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. + Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. - An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. - IEDB - IEDB + An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. + IEDB + IEDB analytical chromatography @@ -47537,11 +50408,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N electron microscopy imaging assay - Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. + Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. - An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. - IEDB - IEDB + An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. + IEDB + IEDB electron microscopy imaging assay @@ -47576,11 +50447,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N immuno staining assay - Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. + Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. - A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. - IEDB - IEDB + A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. + IEDB + IEDB immuno staining assay @@ -47601,13 +50472,13 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - purified material - A mixture of peptide molecules that has been run through an HPLC column to remove 65 + purified material + A mixture of peptide molecules that has been run through an HPLC column to remove 65 - A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component - GROUP: OBI call - OBI conference call - purified material + A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component + GROUP: OBI call + OBI conference call + purified material @@ -47646,11 +50517,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N calorimetric binding assay - A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._ + A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._ - A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. - IEDB - IEDB + A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. + IEDB + IEDB calorimetric binding assay @@ -47712,11 +50583,11 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N antibody binding detection by fluorescence quenching - The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). + The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). - A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). - IEDB - IEDB + A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). + IEDB + IEDB antibody binding detection by fluorescence quenching @@ -47771,6 +50642,17 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + + + + + + + + + + + @@ -47784,10 +50666,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 - A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|inhibition by antigen (~ IC50)|nM + A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|inhibition by antigen (~ IC50)|nM antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 @@ -47815,10 +50697,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 biological activity assay measuring epitope specific Ig-mediated histamine release - A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - histamine release|biological activity + A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + histamine release|biological activity biological activity assay measuring epitope specific Ig-mediated histamine release @@ -47841,10 +50723,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation - A B cell epitope dependent biological activity determination assay that detects antigen activation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - antigen activation|biological activity + A B cell epitope dependent biological activity determination assay that detects antigen activation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + antigen activation|biological activity biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation @@ -47872,10 +50754,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 biological activity assay measuring epitope specific complement-dependent cytotoxicity - A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - complement-dependent cytotoxicity|biological activity + A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + complement-dependent cytotoxicity|biological activity biological activity assay measuring epitope specific complement-dependent cytotoxicity @@ -47903,10 +50785,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity - A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - antibody-dependent cellular cytotoxicity|biological activity + A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + antibody-dependent cellular cytotoxicity|biological activity biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity @@ -47934,10 +50816,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 biological activity assay measuring epitope specific immunoglobulin-mediated neutralization - A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - neutralization |biological activity + A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + neutralization |biological activity biological activity assay measuring epitope specific immunoglobulin-mediated neutralization @@ -47965,10 +50847,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 biological activity assay measuring epitope specific opsonization - A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - opsonization|biological activity + A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + opsonization|biological activity biological activity assay measuring epitope specific opsonization @@ -47980,21 +50862,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + calorimetry assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a calorimetric binding assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|calorimetry + A calorimetric binding assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|calorimetry calorimetry assay measuring binding of a B cell epitope:antibody complex @@ -48006,25 +50898,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + - + + + + + + + electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex - A B cell epitope 3D structure determination assay that uses an electron microscopy imaging assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|electron microscopy + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|electron microscopy electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex @@ -48036,25 +50934,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + - + + + + + + + NMR assay determining the 3D structure of a B cell epitope:antibody complex - A B cell epitope 3D structure determination assay that uses a nuclear magnetic resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|nuclear magnetic resonance (NMR) + A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|nuclear magnetic resonance (NMR) NMR assay determining the 3D structure of a B cell epitope:antibody complex @@ -48066,21 +50970,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + cross blocking assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an antibody cross-blocking assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cross blocking + A cross-blocking assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cross blocking cross blocking assay measuring binding of a B cell epitope:antibody complex @@ -48092,21 +51006,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + RIA measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a radio immuno assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|radio immuno assay (RIA) + A radio immuno assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|radio immuno assay (RIA) RIA measuring binding of a B cell epitope:antibody complex @@ -48118,21 +51042,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + immunoblot assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an immunoblot assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|western blot + An immunoblot assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|western blot immunoblot assay measuring binding of a B cell epitope:antibody complex @@ -48144,21 +51078,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + plasmon resonance assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a surface plasmon resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|surface plasmon resonance (SPR) + A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|surface plasmon resonance (SPR) plasmon resonance assay measuring binding of a B cell epitope:antibody complex @@ -48170,21 +51114,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + immuno staining assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an immuno staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|immuno staining + An immuno staining assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|immuno staining immuno staining assay measuring binding of a B cell epitope:antibody complex @@ -48196,21 +51150,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + immunoprecipitation assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an immunoprecipitation assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|immunoprecipitation + An immunoprecipitation assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|immunoprecipitation immunoprecipitation assay measuring binding of a B cell epitope:antibody complex @@ -48222,21 +51186,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + mass spectrometry assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a mass spectrometry assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|mass spectrometry + A mass spectrometry assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|mass spectrometry mass spectrometry assay measuring binding of a B cell epitope:antibody complex @@ -48248,21 +51222,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + phage display assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a phage display binding assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|phage display + A phage display binding assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|phage display phage display assay measuring binding of a B cell epitope:antibody complex @@ -48274,21 +51258,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + electron microscopy assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an electron microscopy imaging assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|electron microscopy + An electron microscopy imaging assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|electron microscopy electron microscopy assay measuring binding of a B cell epitope:antibody complex @@ -48300,21 +51294,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + ELISA measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunosorbent assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|ELISA + An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|ELISA ELISA measuring binding of a B cell epitope:antibody complex @@ -48326,21 +51330,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + ELISPOT assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunospot assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|ELISPOT + An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|ELISPOT ELISPOT assay measuring binding of a B cell epitope:antibody complex @@ -48352,21 +51366,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + flow cytometry assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a flow cytometry assay. - IEDB - IEDB - qualitative binding|flow cytometry + A flow cytometry assay that detects the binding of an antigen with an antibody. + IEDB + IEDB + qualitative binding|flow cytometry flow cytometry assay measuring binding of a B cell epitope:antibody complex @@ -48389,10 +51413,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 intracellular material detection assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay. - IEDB - IEDB - granzyme A release|intracellular staining + A T cell epitope specific granzyme A release assay that uses an intracellular material detection by flow cytometry assay. + IEDB + IEDB + granzyme A release|intracellular staining intracellular material detection assay measuring epitope specific granzyme A release by T cells @@ -48404,21 +51428,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + chromatography assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an analytical chromatography assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|chromatography + An analytical chromatography assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|chromatography chromatography assay measuring binding of a B cell epitope:antibody complex @@ -48435,16 +51469,29 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + + + + + + + + + + + + + NMR assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|nuclear magnetic resonance (NMR) + A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|nuclear magnetic resonance (NMR) NMR assay measuring binding of a B cell epitope:antibody complex @@ -48467,10 +51514,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 ELISA measuring epitope specific granulysin release by T cells - A T cell epitope specific granulysin release assay that uses an ELISA. - IEDB - IEDB - granulysin release|ELISA + A T cell epitope specific granulysin release assay that uses an ELISA. + IEDB + IEDB + granulysin release|ELISA ELISA measuring epitope specific granulysin release by T cells @@ -48493,10 +51540,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 intracellular material detection assay measuring epitope specific granulysin release by T cells - A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay. - IEDB - IEDB - granulysin release|intracellular staining + A T cell epitope specific granulysin release assay that uses an intracellular material detection by flow cytometry assay. + IEDB + IEDB + granulysin release|intracellular staining intracellular material detection assay measuring epitope specific granulysin release by T cells @@ -48508,11 +51555,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - + @@ -48527,6 +51570,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + + + + + + + + + + + + + @@ -48539,14 +51595,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + - cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|cellular MHC/direct/fluorescence|1/s - cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|cellular MHC/direct/fluorescence|1/s + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex @@ -48557,11 +51614,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - + @@ -48576,6 +51629,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + + + + + + + + + + + + + @@ -48588,14 +51654,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + - cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex - A cell bound MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 - cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection + A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex @@ -48603,63 +51670,72 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - + + + + + - - + + - - - - - - - - - - - - + - - - - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection + + + + + + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 @@ -48698,12 +51774,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 split-ubiquitin assay - Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562 + Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562 - A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. - Marcus Chibucos - Philippe Rocca-Serra - url:https://en.wikipedia.org/wiki/Two-hybrid_screening + A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. + Marcus Chibucos + Philippe Rocca-Serra + url:https://en.wikipedia.org/wiki/Two-hybrid_screening split-ubiquitin assay @@ -48743,12 +51819,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 far-western blot assay - Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 + Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 - An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. - Marcus Chibucos - Philippe Rocca-Serra - PMID:18079728 + An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. + Marcus Chibucos + Philippe Rocca-Serra + PMID:18079728 far-western blot assay @@ -48782,14 +51858,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 RNA protection assay - Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275 - - An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. - Marcus Chibucos - Philippe Rocca-Serra - RNAse protection assay - RPA - PMID:16491611 + Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275 + + An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. + Marcus Chibucos + Philippe Rocca-Serra + RNAse protection assay + RPA + PMID:16491611 RNA protection assay @@ -48823,17 +51899,17 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 electrophoretic mobility shift assay - Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373 - - An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. - Marcus Chibucos - Philippe Rocca-Serra - EMSA - band shift assay - gel mobility shift assay - gel retardation assay - gel shift assay - PMID:6269071 + Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373 + + An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. + Marcus Chibucos + Philippe Rocca-Serra + EMSA + band shift assay + gel mobility shift assay + gel retardation assay + gel shift assay + PMID:6269071 electrophoretic mobility shift assay @@ -48875,10 +51951,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 gene knock-down assay - An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. - Marcus Chibucos - Philippe Rocca-Serra - PMID:17430206 + An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. + Marcus Chibucos + Philippe Rocca-Serra + PMID:17430206 gene knock-down assay @@ -48918,13 +51994,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 nano-cap analysis of gene expression assay - Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 + Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 - A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). - Marcus Chibucos - Philippe Rocca-Serra - nano-CAGE - PMID:20543846 + A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). + Marcus Chibucos + Philippe Rocca-Serra + nano-CAGE + PMID:20543846 nano-cap analysis of gene expression assay @@ -48996,13 +52072,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 cap analysis of gene expression assay - 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 + 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 - A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome - Marcus Chibucos - Philippe Rocca-Serra - CAGE - PMID:14663149 + A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome + Marcus Chibucos + Philippe Rocca-Serra + CAGE + PMID:14663149 cap analysis of gene expression assay @@ -49014,10 +52090,25 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + + + + + + @@ -49026,10 +52117,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 ELISA measuring epitope specific interleukin-17A production by T cells - A T cell epitope specific interleukin-17A production assay that uses an ELISA. - IEDB - IEDB - IL-17A release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. + IEDB + IEDB + IL-17A release|ELISA ELISA measuring epitope specific interleukin-17A production by T cells @@ -49041,21 +52132,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells - An assay of epitope specific interleukin-7 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - IL-7 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells @@ -49076,13 +52183,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - epitope specific granulysin production by T cells + epitope specific granulysin production by T cells - A process of granulysin production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific granulysin production by T cells + A process of granulysin production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific granulysin production by T cells @@ -49102,13 +52209,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - epitope specific granzyme A production by T cells + epitope specific granzyme A production by T cells - A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific granzyme A production by T cells + A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific granzyme A production by T cells @@ -49147,13 +52254,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 yeast 2-hybrid assay - Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486 + Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486 - An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. - Marcus Chibucos - Philippe Rocca-Serra - Y2H - url:https://en.wikipedia.org/wiki/Two-hybrid_screening + An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. + Marcus Chibucos + Philippe Rocca-Serra + Y2H + url:https://en.wikipedia.org/wiki/Two-hybrid_screening yeast 2-hybrid assay @@ -49193,13 +52300,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 Sos-recruitment assay - The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944 + The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944 - A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. - Marcus Chibucos - Philippe Rocca-Serra - SRS - PMID:9154808 + A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. + Marcus Chibucos + Philippe Rocca-Serra + SRS + PMID:9154808 Sos-recruitment assay @@ -49233,13 +52340,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 yeast one-hybrid assay - Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 + Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 - An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. - Marcus Chibucos - Philippe Rocca-Serra - Y1H - PMID:22218861 + An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. + Marcus Chibucos + Philippe Rocca-Serra + Y1H + PMID:22218861 yeast one-hybrid assay @@ -49279,13 +52386,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 bacterial one-hybrid assay - A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 + A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 - An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence - Marcus Chibucos - Philippe Rocca-Serra - B1H - url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system + An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence + Marcus Chibucos + Philippe Rocca-Serra + B1H + url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system bacterial one-hybrid assay @@ -49367,13 +52474,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 chromosome organization assay by fluorescence in-situ hybridization - Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 + Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 - An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity - Marcus Chibucos - Philippe Rocca-Serra - FISH - https://github.com/obi-ontology/obi/issues/788| + An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity + Marcus Chibucos + Philippe Rocca-Serra + https://github.com/obi-ontology/obi/issues/788| chromosome organization assay by fluorescence in-situ hybridization @@ -49401,13 +52507,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 methylation-specific polymerase chain reaction assay - Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 + Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 - An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. - Marcus Chibucos - Philippe Rocca-Serra - MSP - PMID:8790415 + An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. + Marcus Chibucos + Philippe Rocca-Serra + MSP + PMID:8790415 methylation-specific polymerase chain reaction assay @@ -49447,14 +52553,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 amplification of intermethylated sites assay - Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 - - An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. - Marcus Chibucos - Philippe Rocca-Serra - AIMS assay - intermethylated site amplification - PMID:18987810 + Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 + + An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. + Marcus Chibucos + Philippe Rocca-Serra + AIMS assay + intermethylated site amplification + PMID:18987810 amplification of intermethylated sites assay @@ -49500,14 +52606,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 in-situ hybridization assay - Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 - - An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. - Marcus Chibucos - Philippe Rocca-Serra - ISH - in situ hybridization - PMID:9021518 + Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 + + An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. + Marcus Chibucos + Philippe Rocca-Serra + ISH + in situ hybridization + PMID:9021518 in-situ hybridization assay @@ -49525,13 +52631,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 contact representative role - A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. + A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 - Person: Chris Stoeckert + Person: Chris Stoeckert NIAID GSCID-BRC contact representative role @@ -49573,9 +52679,9 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 cytochalasin-induced inhibition of actin polymerization assay - An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). - Marcus Chibucos - Philippe Rocca-Serra + An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). + Marcus Chibucos + Philippe Rocca-Serra cytochalasin-induced inhibition of actin polymerization assay @@ -49621,10 +52727,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific protection from fertility - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - protection from fertility|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + protection from fertility|in vivo assay in vivo assay measuring B cell epitope specific protection from fertility @@ -49656,10 +52762,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific tolerance induction - An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - tolerance|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + tolerance|in vivo assay in vivo assay measuring B cell epitope specific tolerance induction @@ -49691,10 +52797,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific induction of hypersensitivity - An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - hypersensitivity|in vivo assay + An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + hypersensitivity|in vivo assay in vivo assay measuring B cell epitope specific induction of hypersensitivity @@ -49722,10 +52828,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 biological activity assay measuring epitope specific immune complex formation - A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - agglutination|biological activity + A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + agglutination|biological activity biological activity assay measuring epitope specific immune complex formation @@ -49743,10 +52849,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific protection based on survival - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - survival from challenge|in vivo assay + A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + survival from challenge|in vivo assay in vivo assay measuring B cell epitope specific protection based on survival @@ -49769,10 +52875,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific treatment of disease - An efficacy of B cell epitope intervention experiment that detects a decrease in disease. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - decreased disease|in vivo assay + An efficacy of B cell epitope intervention experiment that detects a decrease in disease. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + decreased disease|in vivo assay in vivo assay measuring B cell epitope specific treatment of disease @@ -49795,10 +52901,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 biological activity assay measuring B cell epitope specific in vivo activity - A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - in vivo activity|biological activity + A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + in vivo activity|biological activity biological activity assay measuring B cell epitope specific in vivo activity @@ -49859,12 +52965,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 antibody cross-blocking assay - Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. + Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. - A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. - IEDB - antibody inhibition of antibody binding - IEDB + A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. + IEDB + antibody inhibition of antibody binding + IEDB antibody cross-blocking assay @@ -49908,11 +53014,11 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 immunoprecipitation assay - Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. + Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. - An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. - IEDB - IEDB + An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. + IEDB + IEDB immunoprecipitation assay @@ -49938,12 +53044,29 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + + + + + + + + + + + + + + + + + antigen inhibition assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|inhibition by antigen + A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|inhibition by antigen antigen inhibition assay measuring binding of a B cell epitope:antibody complex @@ -50002,13 +53125,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - immunoglobulin binding to epitope - Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus + immunoglobulin binding to epitope + Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus - a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). - PERSON: Bjoern Peters, Randi Vita - IEDB - immunoglobulin binding to epitope + a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). + PERSON: Bjoern Peters, Randi Vita + IEDB + immunoglobulin binding to epitope @@ -50019,7 +53142,11 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + @@ -50033,13 +53160,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - assay measuring qualitiative binding of a B cell epitope:antibody complex + assay measuring qualitative binding of a B cell epitope:antibody complex - A B cell epitope recognition assay that detects qualitative binding. - IEDB - IEDB - qualitative binding|binding assay - assay measuring qualitiative binding of a B cell epitope:antibody complex + An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output. + IEDB + IEDB + qualitative binding|binding assay + assay measuring qualitative binding of a B cell epitope:antibody complex @@ -50066,10 +53193,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 biological activity assay measuring epitope specific activation of additional immune response in vitro - A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. - IEDB - IEDB - secondary in vitro activity|biological activity + A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. + IEDB + IEDB + secondary in vitro activity|biological activity biological activity assay measuring epitope specific activation of additional immune response in vitro @@ -50097,10 +53224,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 biological activity assay measuring epitope specific antigen inhibition of antibody activity - A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. - IEDB - IEDB - antibody activity inhibition|biological activity + A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. + IEDB + IEDB + antibody activity inhibition|biological activity biological activity assay measuring epitope specific antigen inhibition of antibody activity @@ -50112,7 +53239,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -50130,14 +53257,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - assay measuring B cell epitope specific biological activity + + assay measuring biological activity resulting from B cell epitope:antibody binding - A B cell epitope recognition assay that detects biological activity. - IEDB - IEDB - biological activity|any method - assay measuring B cell epitope specific biological activity + A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope. + IEDB + IEDB + biological activity|any method + assay measuring biological activity resulting from B cell epitope:antibody binding @@ -50146,13 +53273,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - immunoglobulin mediated histamine release + immunoglobulin mediated histamine release - The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. - 4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile. - PERSON: Bjoern Peters, Randi Vita - IEDB - immunoglobulin mediated histamine release + The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. + 4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile. + PERSON: Bjoern Peters, Randi Vita + IEDB + immunoglobulin mediated histamine release @@ -50163,21 +53290,39 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + + + assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope binding constant determination assay that measures the dissociation constant KD. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|binding assay|nM + A B cell epitope binding constant determination assay that measures the dissociation constant KD. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -50189,21 +53334,30 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + - + assay measuring a binding constant of a B cell epitope:antibody complex - A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - binding constant|binding assay + A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + binding constant|binding assay assay measuring a binding constant of a B cell epitope:antibody complex @@ -50226,10 +53380,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific protection from challenge - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - protection from challenge|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + protection from challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge @@ -50252,10 +53406,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 in vivo assay measuring B cell epitope specific disease exacerbation - An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - disease exacerbation|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + disease exacerbation|in vivo assay in vivo assay measuring B cell epitope specific disease exacerbation @@ -50267,11 +53421,11 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 obsolete B cell epitope direct binding assay - A direct binding assay using a assay - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + A direct binding assay using a assay + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - direct binding assay + direct binding assay obsolete B cell epitope direct binding assay true @@ -50293,13 +53447,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific opsonization + B cell epitope specific opsonization - opsonization resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific opsonization + opsonization resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific opsonization @@ -50319,13 +53473,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific immunoglobulin-mediated neutralization + B cell epitope specific immunoglobulin-mediated neutralization - immunoglobulin-mediated neutralization resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific immunoglobulin-mediated neutralization + immunoglobulin-mediated neutralization resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific immunoglobulin-mediated neutralization @@ -50336,11 +53490,11 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 obsolete B cell epitope competitive binding assay - A competitive inhibition of binding assay using a assay - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + A competitive inhibition of binding assay using a assay + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - competitive binding assay + competitive binding assay obsolete B cell epitope competitive binding assay true @@ -50362,13 +53516,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific complement-dependent cytotoxicity + B cell epitope specific complement-dependent cytotoxicity - complement-dependent cytotoxicity resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific complement-dependent cytotoxicity + complement-dependent cytotoxicity resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific complement-dependent cytotoxicity @@ -50388,13 +53542,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific antibody-dependent cellular cytotoxicity + B cell epitope specific antibody-dependent cellular cytotoxicity - antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific antibody-dependent cellular cytotoxicity + antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific antibody-dependent cellular cytotoxicity @@ -50405,21 +53559,39 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + + + assay measuring the on rate [kon] of a B cell epitope:antibody complex - A B cell epitope binding constant determination assay that measures the on rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|binding assay|M^-1s^-1 + A B cell epitope binding constant determination assay that measures the on rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|binding assay|M^-1s^-1 assay measuring the on rate [kon] of a B cell epitope:antibody complex @@ -50431,21 +53603,39 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + + + assay measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope binding constant determination assay that measures the association constant KA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|binding assay|1/nM + A B cell epitope binding constant determination assay that measures the association constant KA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|binding assay|1/nM assay measuring the association constant [KA] of a B cell epitope:antibody complex @@ -50464,13 +53654,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific immune complex formation + B cell epitope specific immune complex formation - immune complex formation resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific immune complex formation + immune complex formation resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific immune complex formation @@ -50481,27 +53671,32 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + - + + + + + + - - - 3D structure determining assay of a 3D B cell epitope:antibody complex + + + 3D molecular structure determination assay of an antigen:antibody complex - A B cell epitope recognition assay that characterizes the 3D structure of an antibody / BCR with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|any method - 3D structure determining assay of a 3D B cell epitope:antibody complex + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|any method + 3D molecular structure determination assay of an antigen:antibody complex @@ -50521,13 +53716,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific hypersensitivity + B cell epitope specific hypersensitivity - hypersensitivity resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific hypersensitivity + hypersensitivity resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific hypersensitivity @@ -50538,21 +53733,39 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + + + assay measuring the off rate [koff] of a B cell epitope:antibody complex - A B cell epitope binding constant determination assay that measures the off rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|binding assay|1/s + A B cell epitope binding constant determination assay that measures the off rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|binding assay|1/s assay measuring the off rate [koff] of a B cell epitope:antibody complex @@ -50564,22 +53777,32 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + - biological activity assay measuring epitope specific hemagglutination inhibition + viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a viral hemagglutination inhibition assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - hemagglutination inhibition|biological activity - biological activity assay measuring epitope specific hemagglutination inhibition + A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding| hemagglutination inhibition + viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex @@ -50599,13 +53822,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - B cell epitope specific histamine secretion mediated by immunoglobulin + B cell epitope specific histamine secretion mediated by immunoglobulin - histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific histamine secretion mediated by immunoglobulin + histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific histamine secretion mediated by immunoglobulin @@ -50616,21 +53839,31 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + quenching assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an antibody binding detection by fluorescence quenching. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|quenching + A fluorescence quenching assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|quenching quenching assay measuring binding of a B cell epitope:antibody complex @@ -50642,10 +53875,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50659,13 +53901,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a radio immuno assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|radio immuno assay (RIA)|nM + A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|radio immuno assay (RIA)|nM RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -50677,10 +53920,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50694,13 +53946,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an enzyme-linked immunosorbent assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|ELISA|nM + An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|ELISA|nM ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -50712,10 +53965,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50729,13 +53991,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an antibody binding detection by fluorescence quenching assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|quenching|nM + A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|quenching|nM quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -50747,10 +54010,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50764,13 +54036,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope equilibrium association constant (KA) determination assay that uses a surface plasmon resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|surface plasmon resonance (SPR)|1/nM + A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|surface plasmon resonance (SPR)|1/nM surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex @@ -50782,10 +54055,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50799,13 +54081,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|surface plasmon resonance (SPR)|nM + A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|surface plasmon resonance (SPR)|nM surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -50817,10 +54100,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50834,13 +54126,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope equilibrium association constant (KA) determination assay that uses an antibody binding detection by fluorescence quenching assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|quenching|1/nM + A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|quenching|1/nM quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex @@ -50852,10 +54145,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50869,13 +54171,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope equilibrium association constant (KA) determination assay that uses a calorimetric binding assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|calorimetry|1/nM + A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|calorimetry|1/nM calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex @@ -50887,10 +54190,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50904,13 +54216,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a calorimetric binding assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|calorimetry|nM + A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|calorimetry|nM calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -50922,10 +54235,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50939,13 +54261,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + ELISA measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope equilibrium association constant (KA) determination assay that uses an enzyme-linked immunosorbent assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|ELISA|1/nM + An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|ELISA|1/nM ELISA measuring the association constant [KA] of a B cell epitope:antibody complex @@ -50957,10 +54280,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -50974,13 +54306,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + RIA measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope equilibrium association constant (KA) determination assay that uses a radio immuno assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|radio immuno assay (RIA)|1/nM + A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|radio immuno assay (RIA)|1/nM RIA measuring the association constant [KA] of a B cell epitope:antibody complex @@ -50992,12 +54325,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 obsolete B cell epitope specific X-ray crystallography assay - A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) + A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) - X-ray crystallography [Ã…] + X-ray crystallography [Ã…] obsolete B cell epitope specific X-ray crystallography assay true @@ -51010,14 +54343,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + - + + + + + + @@ -51031,13 +54369,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex - A B cell epitope 3D structure determination assay that uses an X-ray crystallography assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|x-ray crystallography|angstroms + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex @@ -51049,10 +54388,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -51066,13 +54414,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex - A B cell epitope binding off rate measurement (koff) determination assay that uses a surface plasmon resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|surface plasmon resonance (SPR)|1/s + A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|surface plasmon resonance (SPR)|1/s surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex @@ -51084,10 +54433,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -51101,13 +54459,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex - A B cell epitope binding off rate measurement (koff) determination assay that uses an antibody binding detection by fluorescence quenching assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|quenching|1/s + A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|quenching|1/s quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex @@ -51119,10 +54478,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -51136,13 +54504,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex - A B cell epitope on rate measurement (kon) determination assay that uses a surface plasmon resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|surface plasmon resonance (SPR)|M^-1s^-1 + A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|surface plasmon resonance (SPR)|M^-1s^-1 surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex @@ -51154,10 +54523,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + @@ -51171,13 +54549,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex - A B cell epitope on rate measurement (kon) determination assay that uses an antibody binding detection by fluorescence quenching assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|quenching|M^-1s^-1 + A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|quenching|M^-1s^-1 quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex @@ -51189,21 +54568,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells - An assay of epitope specific interleukin-1 beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells @@ -51215,21 +54610,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells - An assay of epitope specific interleukin-1 alpha production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|ICS + A flow cytometry assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells @@ -51241,21 +54652,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells - An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|ELISPOT ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells @@ -51267,21 +54694,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells - An assay of epitope specific interleukin-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells @@ -51293,21 +54736,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells - An assay of epitope specific interleukin-1 alpha production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|cytometric bead array + A cytometric bead array assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells @@ -51319,21 +54778,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interferon-beta production by T cells - An assay of epitope specific interferon-beta production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|ELISPOT + An enzyme-linked immunospot assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|ELISPOT ELISPOT assay measuring epitope specific interferon-beta production by T cells @@ -51345,21 +54820,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells - An assay of epitope specific interferon-beta production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|ICS + A flow cytometry assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|ICS intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells @@ -51371,21 +54862,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells - An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|ICS + A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|ICS intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells @@ -51397,21 +54904,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-beta production by T cells - An assay of epitope specific interferon-beta production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|ELISA + An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|ELISA ELISA measuring epitope specific interferon-beta production by T cells @@ -51423,21 +54946,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells - An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells @@ -51449,21 +54988,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells - An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|ELISPOT + An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|ELISPOT ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells @@ -51475,21 +55030,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|cytometric bead array + A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -51517,21 +55088,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|ELISPOT + An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -51543,21 +55130,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells @@ -51569,21 +55172,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISPOT assay. - IEDB - IEDB - CCL4/MIP-1b release|ELISPOT + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. + IEDB + IEDB + CCL4/MIP-1b release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -51595,21 +55214,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL12/SDF-1 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL12/SDF-1 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells @@ -51621,21 +55256,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL13/BLC release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL13/BLC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells @@ -51647,21 +55298,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - An assay of epitope specific chemokine (C-X-C motif) ligand 16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL16 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL16 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells @@ -51673,21 +55340,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL21/SLC release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL21/SLC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells @@ -51699,21 +55382,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL22/MDC release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL22/MDC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells @@ -51725,21 +55424,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|cytometric bead array + A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -51751,21 +55466,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - CCL4/MIP-1b release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells. + IEDB + IEDB + CCL4/MIP-1b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells @@ -51777,21 +55508,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells - An assay of epitope specific vascular endothelial growth factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - VEGF release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells @@ -51803,21 +55550,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 19 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL19/MIP-3b release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL19/MIP-3b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells @@ -51829,21 +55592,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|ICS + A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -51917,21 +55696,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells - An assay of epitope specific vascular endothelial growth factor production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - VEGF release|ICS + A flow cytometry assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|ICS intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells @@ -51943,21 +55738,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells - An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISPOT assay. - IEDB - IEDB - VEGF release|ELISPOT + An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|ELISPOT ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells @@ -51969,13 +55780,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -51983,13 +55804,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific interleukin-17F production by T cells + assay measuring epitope specific interleukin-17F production by T cells - An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|biological activity - biological activity assay measuring epitope specific interleukin-17F production by T cells + An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|biological activity + assay measuring epitope specific interleukin-17F production by T cells @@ -52000,13 +55821,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52014,13 +55845,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific interleukin-17A production by T cells + assay measuring epitope specific interleukin-17A production by T cells - An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17A release|biological activity - biological activity assay measuring epitope specific interleukin-17A production by T cells + An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17A release|biological activity + assay measuring epitope specific interleukin-17A production by T cells @@ -52031,13 +55862,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52045,13 +55886,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL21/SLC release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL21/SLC release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells @@ -52062,13 +55903,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52076,13 +55927,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL19/MIP-3b release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL19/MIP-3b release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells @@ -52093,13 +55944,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52107,13 +55968,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. - IEDB - IEDB - CXCL12/SDF-1 release|biological activity - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. + IEDB + IEDB + CXCL12/SDF-1 release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells @@ -52124,13 +55985,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52138,13 +56009,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL22/MDC release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL22/MDC release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells @@ -52155,13 +56026,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52169,13 +56050,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL16 release|biological activity - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL16 release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells @@ -52186,13 +56067,23 @@ is realized in a specimen collection process. - + - + + + + + + + + + + + @@ -52200,13 +56091,13 @@ is realized in a specimen collection process. - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL13/BLC release|biological activity - biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL13/BLC release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells @@ -52217,21 +56108,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|ELISPOT + An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -52243,21 +56150,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|cytometric bead array + A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -52269,21 +56192,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -52295,21 +56234,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|ICS + A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|ICS intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells @@ -52321,21 +56276,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|ELISPOT + An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|ELISPOT ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells @@ -52347,21 +56318,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|ICS + A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|ICS intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -52373,21 +56360,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|ELISPOT + An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells @@ -52399,21 +56402,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells - An assay of epitope specific vascular endothelial growth factor production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - VEGF release|cytometric bead array + A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|cytometric bead array cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells @@ -52425,21 +56444,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - TNF release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells. + IEDB + IEDB + TNF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -52451,21 +56486,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific RANTES production by T cells - An assay of epitope specific RANTES production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|ICS + A flow cytometry assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|ICS intracellular cytokine staining assay measuring epitope specific RANTES production by T cells @@ -52477,21 +56528,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific RANTES production by T cells - An assay of epitope specific RANTES production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|ELISPOT + An enzyme-linked immunospot assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|ELISPOT ELISPOT assay measuring epitope specific RANTES production by T cells @@ -52503,10 +56570,25 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + @@ -52515,10 +56597,10 @@ is realized in a specimen collection process. ELISPOT assay measuring epitope specific lymphotoxin A production by T cells - An assay of epitope specific lymphotoxin A production by T cells that uses an ELISPOT assay. - IEDB - IEDB - lymphotoxin A/TNFb release|ELISPOT + An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. + IEDB + IEDB + lymphotoxin A/TNFb release|ELISPOT ELISPOT assay measuring epitope specific lymphotoxin A production by T cells @@ -52530,21 +56612,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells @@ -52556,10 +56654,25 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + @@ -52568,10 +56681,10 @@ is realized in a specimen collection process. cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells - An assay of epitope specific lymphotoxin A production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - lymphotoxin A/TNFb release|cytometric bead array + A cytometric bead array assay that detects lymphotoxin A production by T cells. + IEDB + IEDB + lymphotoxin A/TNFb release|cytometric bead array cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells @@ -52583,10 +56696,25 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + @@ -52595,10 +56723,10 @@ is realized in a specimen collection process. detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells - An assay of epitope specific lymphotoxin A production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - lymphotoxin A/TNFb release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells. + IEDB + IEDB + lymphotoxin A/TNFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells @@ -52610,21 +56738,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific IP-10 production by T cells - An assay of epitope specific IP-10 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|ELISPOT + An enzyme-linked immunospot assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|ELISPOT ELISPOT assay measuring epitope specific IP-10 production by T cells @@ -52636,21 +56780,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells - An assay of epitope specific IP-10 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|ICS + A flow cytometry assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|ICS intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells @@ -52662,21 +56822,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-9 production by T cells - An assay of epitope specific interleukin-9 production by T cells that uses an ELISPOT assay. - IEDB - IEDB - IL-9 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-9 production by T cells @@ -52688,21 +56864,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells - An assay of epitope specific interleukin-9 production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - IL-9 release|ICS + A flow cytometry assay that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells @@ -52714,21 +56906,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells - An assay of epitope specific interleukin-9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - IL-9 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells @@ -52740,21 +56948,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-8 production by T cells - An assay of epitope specific interleukin-8 production by T cells that uses an ELISPOT assay. - IEDB - IEDB - IL-8 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. + IEDB + IEDB + IL-8 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-8 production by T cells @@ -52766,21 +56990,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells - An assay of epitope specific interleukin-8 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - IL-8 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells. + IEDB + IEDB + IL-8 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells @@ -52792,21 +57032,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-3 production by T cells - An assay of epitope specific interleukin-3 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-3 production by T cells @@ -52818,21 +57074,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-7 production by T cells - An assay of epitope specific interleukin-7 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-7 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-7 release|ELISA ELISA measuring epitope specific interleukin-7 production by T cells @@ -52844,21 +57116,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-7 production by T cells - An assay of epitope specific interleukin-7 production by T cells that uses an ELISPOT assay. - IEDB - IEDB - IL-7 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-7 production by T cells @@ -52870,21 +57158,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells - An assay of epitope specific interleukin-7 production by T cells that uses an intracellular cytokine staining assay. - IEDB - IEDB - IL-7 release|ICS + A flow cytometry assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells @@ -52896,21 +57200,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells - An assay of epitope specific interleukin-27 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|ICS + A flow cytometry assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells @@ -52922,21 +57242,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-3 production by T cells - An assay of epitope specific interleukin-3 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|cytometric bead array + A cytometric bead array assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-3 production by T cells @@ -52948,21 +57284,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells - An assay of epitope specific interleukin-3 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells @@ -52990,10 +57342,10 @@ is realized in a specimen collection process. biological activity assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. - IEDB - IEDB - granzyme A release|biological activity + A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. + IEDB + IEDB + granzyme A release|biological activity biological activity assay measuring epitope specific granzyme A release by T cells @@ -53021,10 +57373,10 @@ is realized in a specimen collection process. biological activity assay measuring epitope specific granulysin release by T cells - A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. - IEDB - IEDB - granulysin release|biological activity + A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. + IEDB + IEDB + granulysin release|biological activity biological activity assay measuring epitope specific granulysin release by T cells @@ -53036,21 +57388,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-27 production by T cells - An assay of epitope specific interleukin-27 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|cytometric bead array + A cytometric bead array assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-27 production by T cells @@ -53062,21 +57430,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells - An assay of epitope specific interleukin-23 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|ICS + A flow cytometry assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells @@ -53088,21 +57472,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-27 production by T cells - An assay of epitope specific interleukin-27 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-27 production by T cells @@ -53114,21 +57514,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-27 production by T cells - An assay of epitope specific interleukin-27 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|ELISA ELISA measuring epitope specific interleukin-27 production by T cells @@ -53140,21 +57556,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells - An assay of epitope specific interleukin-18 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells @@ -53178,10 +57610,10 @@ is realized in a specimen collection process. epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 13 production by T cells @@ -53193,21 +57625,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-18 production by T cells - An assay of epitope specific interleukin-18 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-18 production by T cells @@ -53231,10 +57679,10 @@ is realized in a specimen collection process. epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 12 production by T cells @@ -53258,10 +57706,10 @@ is realized in a specimen collection process. epitope specific chemokine (C-C motif) ligand 22 production by T cells - A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 22 production by T cells @@ -53285,10 +57733,10 @@ is realized in a specimen collection process. epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 16 production by T cells @@ -53300,21 +57748,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-22 production by T cells - An assay of epitope specific interleukin-22 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-22 production by T cells @@ -53326,21 +57790,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-23 production by T cells - An assay of epitope specific interleukin-23 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-23 production by T cells @@ -53364,10 +57844,10 @@ is realized in a specimen collection process. epitope specific chemokine (C-C motif) ligand 21 production by T cells - A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 21 production by T cells @@ -53379,21 +57859,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells - An assay of epitope specific interleukin-18 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ICS + A flow cytometry assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells @@ -53417,10 +57913,10 @@ is realized in a specimen collection process. epitope specific chemokine (C-C motif) ligand 19 production by T cells - A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 19 production by T cells @@ -53432,21 +57928,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-21 production by T cells - An assay of epitope specific interleukin-21 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-21 production by T cells @@ -53458,21 +57970,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -53484,21 +58012,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|cytometric bead array + A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -53510,21 +58054,37 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|ELISPOT + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells @@ -53536,10 +58096,25 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + @@ -53548,10 +58123,10 @@ is realized in a specimen collection process. ELISPOT assay measuring epitope specific interleukin-17F production by T cells - A T cell epitope specific interleukin-17F production assay that uses an ELISPOT. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-17F production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17F production by T cells @@ -53563,10 +58138,25 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + @@ -53575,10 +58165,10 @@ is realized in a specimen collection process. ELISA measuring epitope specific interleukin-17F production by T cells - A T cell epitope specific interleukin-17F production assay that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|ELISA ELISA measuring epitope specific interleukin-17F production by T cells @@ -53590,10 +58180,25 @@ is realized in a specimen collection process. - + - - + + + + + + + + + + + + + + + + + @@ -53602,10 +58207,10 @@ is realized in a specimen collection process. detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells - A T cell epitope specific interleukin-17F production assay that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells @@ -53617,22 +58222,37 @@ is realized in a specimen collection process. - + - - - - - + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-17A production by T cells - A T cell epitope specific interleukin-17A production assay that uses an ELISPOT. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17A release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-17A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17A release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17A production by T cells @@ -53671,21 +58291,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-18 production by T cells - An assay of epitope specific interleukin-18 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|cytometric bead array + A cytometric bead array assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-18 production by T cells @@ -53697,21 +58333,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells - An assay of epitope specific interleukin-16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells @@ -53723,21 +58375,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-16 production by T cells - An assay of epitope specific interleukin-16 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|ELISA ELISA measuring epitope specific interleukin-16 production by T cells @@ -53749,21 +58417,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-16 production by T cells - An assay of epitope specific interleukin-16 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-16 production by T cells @@ -53775,21 +58459,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells - An assay of epitope specific interleukin-16 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|ICS + A flow cytometry assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells @@ -53801,10 +58501,25 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + @@ -53813,10 +58528,10 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells - A T cell epitope specific interleukin-17A production assay that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17A release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17A release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells @@ -53828,21 +58543,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells - An assay of epitope specific interleukin-1 beta production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|ICS + A flow cytometry assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells @@ -53854,21 +58585,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells - An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISPOT assay. - IEDB - IEDB - IL-1b release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. + IEDB + IEDB + IL-1b release|ELISPOT ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells @@ -53880,21 +58627,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells - An assay of epitope specific interleukin-15 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|RNA/DNA detection detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells @@ -53906,21 +58669,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-12 production by T cells - An assay of epitope specific interleukin-12 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-12 production by T cells @@ -53932,21 +58711,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells - An assay of epitope specific interleukin-15 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|ICS + A flow cytometry assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells @@ -53958,21 +58753,37 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-15 production by T cells - An assay of epitope specific interleukin-15 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-15 production by T cells @@ -54072,15 +58883,15 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten chromatin interaction analysis by paired-end tag sequencing assay - Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] - - An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. - Chris Stoeckert - Jie Zheng - Venkat Malladi - ChIA-PET - ChIA-PET assay - url:http://en.wikipedia.org/wiki/ChIA-PET + Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] + + An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. + Chris Stoeckert + Jie Zheng + Venkat Malladi + ChIA-PET + ChIA-PET assay + url:http://en.wikipedia.org/wiki/ChIA-PET chromatin interaction analysis by paired-end tag sequencing assay @@ -54091,15 +58902,15 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten structural analysis by paired-end tag sequencing assay - Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] - - An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. - Chris Stoeckert - Jie Zheng - Venkat Malladi - DNA-PET - DNA-PET assay - PMID:23029419 + Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] + + An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. + Chris Stoeckert + Jie Zheng + Venkat Malladi + DNA-PET + DNA-PET assay + PMID:23029419 structural analysis by paired-end tag sequencing assay @@ -54193,15 +59004,15 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten transcript analysis by paired-end tag sequencing assay - Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] - - A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. - Chris Stoeckert - Jie Zheng - Venkat Malladi - RNA-PET - RNA-PET assay - PMID:22113299 + Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] + + A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. + Chris Stoeckert + Jie Zheng + Venkat Malladi + RNA-PET + RNA-PET assay + PMID:22113299 transcript analysis by paired-end tag sequencing assay @@ -54340,13 +59151,13 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten DNase I hypersensitive sites sequencing assay - Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] + Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] - An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. - Chris Stoeckert - Jie Zheng - Venkat Malladi - url:http://en.wikipedia.org/wiki/DNase-Seq + An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. + Chris Stoeckert + Jie Zheng + Venkat Malladi + url:http://en.wikipedia.org/wiki/DNase-Seq DNase I hypersensitive sites sequencing assay @@ -54491,15 +59302,15 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay - Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] - - An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - RIP-seq - RIP-seq assay - PMID:21172659 + Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] + + An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + RIP-seq + RIP-seq assay + PMID:21172659 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay @@ -54605,16 +59416,16 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten cross-linking immunoprecipitation high-throughput sequencing assay - Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] - - An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. - Chris Stoeckert - Jie Zheng - Venkat Malladi - CLIP-seq - CLIP-seq assay - HITS-CLIP - PMID:18978773 + Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] + + An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. + Chris Stoeckert + Jie Zheng + Venkat Malladi + CLIP-seq + CLIP-seq assay + HITS-CLIP + PMID:18978773 cross-linking immunoprecipitation high-throughput sequencing assay @@ -54689,15 +59500,15 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten formaldehyde-assisted isolation of regulatory elements assay - Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] - - An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. - Chris Stoeckert - Jie Zheng - Venkat Malladi - FAIRE-seq - FAIRE-seq assay - url:http://en.wikipedia.org/wiki/FAIRE-Seq + Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] + + An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. + Chris Stoeckert + Jie Zheng + Venkat Malladi + FAIRE-seq + FAIRE-seq assay + url:http://en.wikipedia.org/wiki/FAIRE-Seq formaldehyde-assisted isolation of regulatory elements assay @@ -54808,15 +59619,15 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten methylation-sensitive restriction enzyme sequencing assay - Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] - - An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. - Chris Stoeckert - Jie Zheng - Venkat Malladi - MRE-seq - MRE-seq assay - PMID:20613842 + Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] + + An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. + Chris Stoeckert + Jie Zheng + Venkat Malladi + MRE-seq + MRE-seq assay + PMID:20613842 methylation-sensitive restriction enzyme sequencing assay @@ -54839,16 +59650,16 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten reduced representation bisulfite sequencing assay - Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] - - A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. - Chris Stoeckert - Jie Zheng - Venkat Malladi - RRBS - RRBS assay - reduced representation bisulfite-seq - PMC:1258174 + Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] + + A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. + Chris Stoeckert + Jie Zheng + Venkat Malladi + RRBS + RRBS assay + reduced representation bisulfite-seq + PMC:1258174 reduced representation bisulfite sequencing assay @@ -54889,18 +59700,18 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten shotgun bisulfite-seq assay - Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. - - A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Shotgun bisulfite sequencing - WGBS - WGSBS - whole genome bisulfite sequencing - whole-genome shotgun bisulfite sequencing - PMID:18278030 + Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. + + A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Shotgun bisulfite sequencing + WGBS + WGSBS + whole genome bisulfite sequencing + whole-genome shotgun bisulfite sequencing + PMID:18278030 shotgun bisulfite-seq assay @@ -55000,14 +59811,14 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay - Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] - - An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - RAMPAGE - PMID:22936248 + Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] + + An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + RAMPAGE + PMID:22936248 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay @@ -55025,9 +59836,9 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten assay array - A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. - PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Penn Group + A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. + PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Penn Group assay array @@ -55062,14 +59873,14 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - secondary cultured cell + secondary cultured cell - A cultured cell that has been passaged or derives from a cell that has been passaged in culture. - The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + A cultured cell that has been passaged or derives from a cell that has been passaged in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush - PERSON: Matthew Brush - A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. - secondary cultured cell + PERSON: Matthew Brush + A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. + secondary cultured cell @@ -55144,9 +59955,9 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo Illumina BeadChip - An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. - PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi - http://www.illumina.com/technology/beadarray_technology.ilmn + An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. + PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi + http://www.illumina.com/technology/beadarray_technology.ilmn Illumina BeadChip @@ -55199,9 +60010,9 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo Illumina methylation BeadChip - A BeadChip made for an analyte assay that generates information about DNA methylation. - PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Penn Group + A BeadChip made for an analyte assay that generates information about DNA methylation. + PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Penn Group Illumina methylation BeadChip @@ -55219,9 +60030,9 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo LSRFortessa X-20 - A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. - Anna Maria Masci - http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg + A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. + Anna Maria Masci + http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg LSRFortessa X-20 @@ -55350,12 +60161,12 @@ PMID: 23587118. - cultured immune cell population + cultured immune cell population - a cultured cell population comprised of a single type of immune system cell - MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures. + a cultured cell population comprised of a single type of immune system cell + MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures. PERSON:Matthew Brush - immune cell culture sample + immune cell culture sample PERSON:Matthew Brush cultured immune cell population @@ -55385,13 +60196,13 @@ PMID: 23587118. - cell culture + cell culture - A material entity comprised of cultured cells and the media in which they are being propagated or stored. - PERSON:Matthew Brush + A material entity comprised of cultured cells and the media in which they are being propagated or stored. + PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) - A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. - cell culture + A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. + cell culture @@ -56343,10 +61154,10 @@ In regard to the statement that reagents are 'distinct' from the speci - cancer cell line + cancer cell line - An immortal cell line derived from a transformed cell that was part of a malignant tumor. - cancer cell line + An immortal cell line derived from a transformed cell that was part of a malignant tumor. + cancer cell line @@ -56361,10 +61172,10 @@ In regard to the statement that reagents are 'distinct' from the speci - immortalizing cell line transformation + immortalizing cell line transformation - a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture - immortalizing cell line transformation + a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture + immortalizing cell line transformation @@ -56426,11 +61237,11 @@ The following are NOT conclusions based on data: data themselves; results from p - primary cell culture + primary cell culture - A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. - PERSON:Matthew Brush - OBI-CLO Alignment Working Group (Spring 2013) + A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. + PERSON:Matthew Brush + OBI-CLO Alignment Working Group (Spring 2013) primary cell culture @@ -56446,12 +61257,12 @@ The following are NOT conclusions based on data: data themselves; results from p - cell line culture + cell line culture - A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. - PERSON:Matthew Brush - OBI-CLO Alignment Working Group (Spring 2013) - A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. + A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. + PERSON:Matthew Brush + OBI-CLO Alignment Working Group (Spring 2013) + A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. cell line culture @@ -56461,10 +61272,10 @@ The following are NOT conclusions based on data: data themselves; results from p - cell freezing medium + cell freezing medium - A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. - PERSON: Matthew Brush + A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. + PERSON: Matthew Brush cell freezing medium @@ -56655,15 +61466,15 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ DNA replication timing by array assay - Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] - - An assay which quantifies the timing of DNA replication as a function of genome position using array technology. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Repli-chip - Repli-chip assay - PMID:18842067 + Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] + + An assay which quantifies the timing of DNA replication as a function of genome position using array technology. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Repli-chip + Repli-chip assay + PMID:18842067 DNA replication timing by array assay @@ -56784,15 +61595,15 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ RNA-binding protein immunoprecipitation array profiling assay - Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] - - An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - RIP-chip - RIP-chip assay - PMID:21125495 + Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] + + An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + RIP-chip + RIP-chip assay + PMID:21125495 RNA-binding protein immunoprecipitation array profiling assay @@ -56904,15 +61715,15 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ Carbon-copy chromosome conformation capture assay - van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] - - An assay that measures the organization of chromosomes at the genome-wide scale. - Chris Stoeckert - Jie Zheng - Venkat Malladi - 5C - 5C assay - PMID:16954542 + van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] + + An assay that measures the organization of chromosomes at the genome-wide scale. + Chris Stoeckert + Jie Zheng + Venkat Malladi + 5C + 5C assay + PMID:16954542 Carbon-copy chromosome conformation capture assay @@ -57046,15 +61857,15 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ DNA replication timing by sequencing assay - Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280] - - An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Repli-seq - Repli-seq assay - PMID:19966280 + Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280] + + An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Repli-seq + Repli-seq assay + PMID:19966280 DNA replication timing by sequencing assay @@ -57089,13 +61900,13 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ RNA-binding protein immunoprecipitation tiling array profiling assay - Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] + Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] - An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - PMID:21125495 + An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + PMID:21125495 RNA-binding protein immunoprecipitation tiling array profiling assay @@ -57193,17 +62004,17 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ microRNA profiling by high throughput sequencing assay - Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 - - A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. - Chris Stoeckert - Jie Zheng - Venkat Malladi - miRNA-HTS - miRNA-seq - microRNA-seq - microRNA-seq assay - url:http://www.ebi.ac.uk/efo/EFO_0002896 + Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 + + A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. + Chris Stoeckert + Jie Zheng + Venkat Malladi + miRNA-HTS + miRNA-seq + microRNA-seq + microRNA-seq assay + url:http://www.ebi.ac.uk/efo/EFO_0002896 microRNA profiling by high throughput sequencing assay @@ -57212,6 +62023,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ + @@ -57284,13 +62096,13 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ protein sequencing by tandem mass spectrometry assay - Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] + Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] - A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. - Chris Stoeckert - Jie Zheng - Venkat Malladi - PMID:3462691 + A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. + Chris Stoeckert + Jie Zheng + Venkat Malladi + PMID:3462691 protein sequencing by tandem mass spectrometry assay @@ -57383,15 +62195,15 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ micrococcal nuclease digestion followed by high throughput sequencing assay - Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] - - An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease - Chris Stoeckert - Jie Zheng - Venkat Malladi - MNase-seq - MNase-seq assay - PMID:17038564 + Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] + + An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease + Chris Stoeckert + Jie Zheng + Venkat Malladi + MNase-seq + MNase-seq assay + PMID:17038564 micrococcal nuclease digestion followed by high throughput sequencing assay @@ -57444,15 +62256,15 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ chromatin immunoprecipitation with exonuclease sequencing assay - Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] - - A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site - Bjoern Peters - Chris Stoeckert - Jie Zheng - Venkat Malladi - ChIP-exo assay - PMID:22153082 + Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] + + A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site + Bjoern Peters + Chris Stoeckert + Jie Zheng + Venkat Malladi + ChIP-exo assay + PMID:22153082 chromatin immunoprecipitation with exonuclease sequencing assay @@ -57515,13 +62327,13 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ microRNA profiling assay - A transcription profiling assay that quantifies the microRNA species within a biological sample. - Chris Stoeckert - Jie Zheng - Venkat Malladi - miRNA expression assay - microRNA expression assay - PMID: 23382819 + A transcription profiling assay that quantifies the microRNA species within a biological sample. + Chris Stoeckert + Jie Zheng + Venkat Malladi + miRNA expression assay + microRNA expression assay + PMID: 23382819 microRNA profiling assay @@ -57774,12 +62586,12 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - molecular-labeled material + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay - PERSON:Matthew Brush + PERSON:Matthew Brush OBI developer call, 3-12-12 - molecular-labeled material + molecular-labeled material @@ -58229,13 +63041,13 @@ PMID: 23587118. ChIP assay - PMID: 6379641 + PMID: 6379641 - An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed - Bjoern Peters - Philippe Rocca-Serra - chromatin immunoprecipitation assay - url:https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation + An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed + Bjoern Peters + Philippe Rocca-Serra + chromatin immunoprecipitation assay + url:https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation ChIP assay @@ -58280,11 +63092,11 @@ PMID: 23587118. assay using chromatin immunoprecipitation - http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html + http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html - An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation - Philippe Rocca-Serra - http://sourceforge.net/p/obi/obi-terms/707/ + An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation + Philippe Rocca-Serra + http://sourceforge.net/p/obi/obi-terms/707/ assay using chromatin immunoprecipitation @@ -58323,9 +63135,9 @@ PMID: 23587118. hardware testing design - A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. - Person: Jie Zheng - MO_734 hardware_variation_design + A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. + Person: Jie Zheng + MO_734 hardware_variation_design hardware testing design @@ -58335,13 +63147,13 @@ PMID: 23587118. - systematic review study design - Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ - The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ + systematic review study design + Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ + The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ - A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. - PERSON: Bill Hogan - systematic review study design + A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. + PERSON: Bill Hogan + systematic review study design @@ -58399,15 +63211,15 @@ PMID: 23587118. taxonomic diversity assessment by targeted gene survey - PMID:20679230 - PMID:25367129 - - An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. - Philippe Rocca-Serra - environmental gene survey - targeted gene survey - targeted gene survey DNA barcoding - OBI + PMID:20679230 + PMID:25367129 + + An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. + Philippe Rocca-Serra + environmental gene survey + targeted gene survey + targeted gene survey DNA barcoding + OBI taxonomic diversity assessment by targeted gene survey @@ -58495,12 +63307,12 @@ PMID: 23587118. - decision analysis study design + decision analysis study design - a study design that has a decision analysis objective specification as part - PERSON: Bill Hogan - PERSON: Bill Hogan - decision analysis study design + a study design that has a decision analysis objective specification as part + PERSON: Bill Hogan + PERSON: Bill Hogan + decision analysis study design @@ -58637,16 +63449,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Ion 316 Chip v2 + Ion 316 Chip v2 - An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. - Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ - PERSON: Sagar Jain - Ion 316 Chip - Ion PGM 316 Chip - Ion PGM 316 Chip v2 - http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html - Ion 316 Chip v2 + An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. + Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ + PERSON: Sagar Jain + Ion 316 Chip + Ion PGM 316 Chip + Ion PGM 316 Chip v2 + http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html + Ion 316 Chip v2 @@ -58655,16 +63467,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Ion 318 Chip v2 + Ion 318 Chip v2 - An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. - Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ - PERSON: Sagar Jain - Ion 318 Chip - Ion PGM 318 Chip - Ion PGM 318 Chip v2 - http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html - Ion 318 Chip v2 + An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. + Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ + PERSON: Sagar Jain + Ion 318 Chip + Ion PGM 318 Chip + Ion PGM 318 Chip v2 + http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html + Ion 318 Chip v2 @@ -58673,16 +63485,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - ion semiconductor chip + ion semiconductor chip - An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. - Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ - PERSON: Sagar Jain - ion chip - ion integrated circuit - ion semiconductor - http://www.thefreedictionary.com/Semiconductor+chip - ion semiconductor chip + An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. + Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ + PERSON: Sagar Jain + ion chip + ion integrated circuit + ion semiconductor + http://www.thefreedictionary.com/Semiconductor+chip + ion semiconductor chip @@ -58691,16 +63503,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Ion 314 Chip v2 + Ion 314 Chip v2 - An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. - Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ - PERSON: Sagar Jain - Ion 314 Chip - Ion PGM 314 Chip - Ion PGM 314 Chip v2 - http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html - Ion 314 Chip v2 + An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. + Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ + PERSON: Sagar Jain + Ion 314 Chip + Ion PGM 314 Chip + Ion PGM 314 Chip v2 + http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html + Ion 314 Chip v2 @@ -58734,11 +63546,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. hydrogen/deuterium exchange footprinting assay - Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. + Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. - A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. - IEDB - IEDB + A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. + IEDB + IEDB hydrogen/deuterium exchange footprinting assay @@ -58788,11 +63600,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. cytometry assay - An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. + An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. - An assay that counts and/or measures characteristics of cells. - IEDB - IEDB + An assay that counts and/or measures characteristics of cells. + IEDB + IEDB cytometry assay @@ -58858,9 +63670,9 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. immunoblot assay - An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. - IEDB - IEDB + An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. + IEDB + IEDB immunoblot assay @@ -58878,9 +63690,9 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. fluorescence quenching binding assay - A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. - IEDB - IEDB + A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. + IEDB + IEDB fluorescence quenching binding assay @@ -58925,12 +63737,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vivo intervention experiment - Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. + Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. - An assay in which the effect of a targeted process (the intervention) on an organism is tested. - The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. - IEDB - IEDB + An assay in which the effect of a targeted process (the intervention) on an organism is tested. + The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. + IEDB + IEDB in vivo intervention experiment @@ -58941,12 +63753,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. disease exacerbation in vivo intervention experiment - Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. + Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. - An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. - Should have data about disease severity as readout; could just use disease for now - IEDB - IEDB + An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. + Should have data about disease severity as readout; could just use disease for now + IEDB + IEDB disease exacerbation in vivo intervention experiment @@ -58957,12 +63769,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. protection from challenge in vivo intervention experiment - Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. + Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. - An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. - should have challenge as intervention - IEDB - IEDB + An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. + should have challenge as intervention + IEDB + IEDB protection from challenge in vivo intervention experiment @@ -58973,12 +63785,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. tolerance induction intervention experiment - Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. + Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. - An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. - should have tolerance induction as intervention - IEDB - IEDB + An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. + should have tolerance induction as intervention + IEDB + IEDB tolerance induction intervention experiment @@ -58989,12 +63801,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. treatment intervention experiment - Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. + Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. - An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. - should have treatment as intervention - IEDB - IEDB + An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. + should have treatment as intervention + IEDB + IEDB treatment intervention experiment @@ -59034,11 +63846,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. microarray assay - Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. + Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. - An analyte assay where binding of the analyte to immobilized matrix is measured. - IEDB - IEDB + An analyte assay where binding of the analyte to immobilized matrix is measured. + IEDB + IEDB microarray assay @@ -59110,11 +63922,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. immunohistochemistry - Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. + Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. - An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. - IEDB - IEDB + An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. + IEDB + IEDB immunohistochemistry @@ -59126,11 +63938,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + @@ -59146,10 +63967,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. assay measuring the association constant [KA] of a MHC:ligand complex - A MHC binding constant determination assay measuring equilibrium association constant (KA). - IEDB - IEDB - association constant KA|binding assay|1/M + A MHC binding constant determination assay measuring equilibrium association constant (KA). + IEDB + IEDB + association constant KA|binding assay|1/M assay measuring the association constant [KA] of a MHC:ligand complex @@ -59161,11 +63982,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + @@ -59181,10 +64011,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. assay measuring the dissociation constant [KD] of a MHC:ligand complex - A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). - IEDB - IEDB - dissociation constant KD|binding assay|nM + A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). + IEDB + IEDB + dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a MHC:ligand complex @@ -59196,11 +64026,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + @@ -59229,6 +64055,19 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + @@ -59241,14 +64080,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation. - IEDB - IEDB - dissociation constant KD|purified MHC/direct/radioactivity|nM - purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + IEDB + IEDB + dissociation constant KD|purified MHC/direct/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex @@ -59259,21 +64099,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + assay measuring the half life of a MHC:ligand complex - A MHC binding constant determination assay measuring half life of binding. - IEDB - IEDB - half life|binding assay|min + A MHC binding constant determination assay measuring half life of binding. + IEDB + IEDB + half life|binding assay|min assay measuring the half life of a MHC:ligand complex @@ -59285,10 +64134,19 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + + + @@ -59302,13 +64160,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex - A MHC binding constant determination assay measuring half maximal effective concentration (EC50). - IEDB - IEDB - half maximal effective concentration (EC50)|binding assay|nM + A MHC binding constant determination assay measuring half maximal effective concentration (EC50). + IEDB + IEDB + half maximal effective concentration (EC50)|binding assay|nM assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex @@ -59320,21 +64178,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + + + - + assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex - A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). - IEDB - IEDB - half maximal inhibitory concentration (IC50)|binding assay|nM + A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). + IEDB + IEDB + half maximal inhibitory concentration (IC50)|binding assay|nM assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex @@ -59346,11 +64213,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + @@ -59366,10 +64242,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. assay measuring the off rate measurement [koff] of a MHC:ligand complex - A MHC binding constant determination assay measuring binding off rate measurement data item (koff). - IEDB - IEDB - off rate|binding assay|1/s + A MHC binding constant determination assay measuring binding off rate measurement data item (koff). + IEDB + IEDB + off rate|binding assay|1/s assay measuring the off rate measurement [koff] of a MHC:ligand complex @@ -59381,21 +64257,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex - A MHC binding constant determination assay measuring binding on rate (kon). - IEDB - IEDB - on rate|binding assay|nM^-1s^-1 + A MHC binding constant determination assay measuring binding on rate (kon). + IEDB + IEDB + on rate|binding assay|nM^-1s^-1 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex @@ -59407,10 +64292,19 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + @@ -59424,13 +64318,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex - A B cell epitope equilibrium association constant (KA) determination assay that uses an analytical chromatography assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|chromatography|1/nM + An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|chromatography|1/nM chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex @@ -59442,10 +64337,19 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + @@ -59459,13 +64363,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an analytical chromatography assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|chromatography|nM + An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|chromatography|nM chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -59477,21 +64382,31 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex - A footprinting assay that uses hydrogen/deuterium exchange to measure B cell epitope qualitative binding to antibody. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - qualitative binding|hydrogen/deuterium exchange footprinting assay + A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|hydrogen/deuterium exchange footprinting assay hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex @@ -59503,21 +64418,31 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + immunohistochemistry assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses an immunohistochemistry assay. - IEDB - IEDB - qualitative binding|immunohistochemistry + A immunohistochemistry assay that detects the binding of an antigen with an antibody. + IEDB + IEDB + qualitative binding|immunohistochemistry immunohistochemistry assay measuring binding of a B cell epitope:antibody complex @@ -59529,27 +64454,32 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + - + + + + + + - - - 3D structure determining assay of a T cell epitope:MHC:TCR complex + + + 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex - A T cell epitope recognition assay that uses a 3D structure determination of bound complex assay. - IEDB - IEDB - 3D structure|any method - 3D structure determining assay of a T cell epitope:MHC:TCR complex + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex. + IEDB + IEDB + 3D structure|any method + 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex @@ -59559,13 +64489,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Genome Analyzer IIx - Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 + Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 - An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina GA IIx - Illumina Genome Analyzer IIx - ENCODE group + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina GA IIx + Illumina Genome Analyzer IIx + ENCODE group Genome Analyzer IIx @@ -59582,12 +64512,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Illumina HiSeq 2000 - Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 + Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng - HiSeq 2000 - http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng + HiSeq 2000 + http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 2000 @@ -59604,12 +64534,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Illumina HiSeq 2500 - Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - HiSeq 2500 - http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + HiSeq 2500 + http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Illumina HiSeq 2500 @@ -59626,12 +64556,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. MiSeq - Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] + Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] - A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina MiSeq - http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf + A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng + Illumina MiSeq + http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf MiSeq @@ -59642,12 +64572,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Methylation 450K BeadChip - Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 + Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 - A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina Infinium Human Methylation 450K BeadChip - http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn + A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina Infinium Human Methylation 450K BeadChip + http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Methylation 450K BeadChip @@ -59658,12 +64588,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Methylation 27K BeadChip - Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 + Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 - A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina Infinium Human Methylation 27K BeadChip - http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf + A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina Infinium Human Methylation 27K BeadChip + http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Methylation 27K BeadChip @@ -59674,12 +64604,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. 1M-Duo Infinium HD BeadChip - Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 + Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 - A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina Human 1M-Duo Infinium HD BeadChip - http://www.illumina.com/technology/infinium_hd_assay.ilmn + A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina Human 1M-Duo Infinium HD BeadChip + http://www.illumina.com/technology/infinium_hd_assay.ilmn 1M-Duo Infinium HD BeadChip @@ -59696,12 +64626,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. SOLiD 3 Plus System - Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 + Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 - A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Applied Biosystems SOLiD 3 Plus System - http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf + A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Applied Biosystems SOLiD 3 Plus System + http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf SOLiD 3 Plus System @@ -59718,12 +64648,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Mouse 385K Whole Genome CGH Tiling Array - Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ + Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Mouse 385K Whole Genome CGH Tiling Array - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Mouse 385K Whole Genome CGH Tiling Array + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Mouse 385K Whole Genome CGH Tiling Array @@ -59740,12 +64670,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Mouse 3x720K Whole Genome CGH Tiling Array - Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 + Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Mouse 3x720K Whole Genome CGH Tiling Array @@ -59762,12 +64692,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human 3x720K Whole Genome CGH Tiling Array - Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 + Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Human 3x720K Whole Genome CGH Tiling Array - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Human 3x720K Whole Genome CGH Tiling Array + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Human 3x720K Whole Genome CGH Tiling Array @@ -59784,12 +64714,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human 2.1M Whole-Genome CGH Tiling Array v2.0 - Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 + Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Human 2.1M Whole-Genome CGH Tiling Array v2.0 @@ -59806,12 +64736,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. PacBio RS II - Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 - A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Pacific Biosciences RS II - http://www.pacificbiosciences.com/products/ + A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Pacific Biosciences RS II + http://www.pacificbiosciences.com/products/ PacBio RS II @@ -59828,11 +64758,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. nCounter Human miRNA Expression array - Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 - A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. - https://www.nanostring.com/products/mirna-assays/mirna-panels + A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. + https://www.nanostring.com/products/mirna-assays/mirna-panels nCounter Human miRNA Expression array @@ -59929,11 +64859,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. DNA methylation profiling by ChIP-chip assay - An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. - Chris Stoeckert - Jie Zheng - DNA methylation ChIP-chip - Penn group + An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. + Chris Stoeckert + Jie Zheng + DNA methylation ChIP-chip + Penn group DNA methylation profiling by ChIP-chip assay @@ -59981,11 +64911,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. transcription profiling by MPSS assay - A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). - Chris Stoeckert - Jie Zheng - expression MPSS - url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing + A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). + Chris Stoeckert + Jie Zheng + expression MPSS + url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing transcription profiling by MPSS assay @@ -60099,11 +65029,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. histone modification identification by ChIP-chip assay - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-chip - Penn group + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. + Chris Stoeckert + Jie Zheng + histone modification ChIP-chip + Penn group histone modification identification by ChIP-chip assay @@ -60217,11 +65147,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. histone modification identification by ChIP-Seq assay - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-Seq - Penn group + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. + Chris Stoeckert + Jie Zheng + histone modification ChIP-Seq + Penn group histone modification identification by ChIP-Seq assay @@ -60335,11 +65265,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. transcription factor binding site identification by ChIP-chip assay - A transcription factor binding site assay that utilizes ChIP-chip technology. - Chris Stoeckert - Jie Zheng - TF Binding ChIP-chip - Penn group + A transcription factor binding site assay that utilizes ChIP-chip technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-chip + Penn group transcription factor binding site identification by ChIP-chip assay @@ -60453,11 +65383,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. transcription factor binding site identification by ChIP-Seq assay - A transcription factor binding site assay that utilizes ChIP-seq technology. - Chris Stoeckert - Jie Zheng - TF Binding ChIP-Seq - Penn group + A transcription factor binding site assay that utilizes ChIP-seq technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-Seq + Penn group transcription factor binding site identification by ChIP-Seq assay @@ -60480,10 +65410,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. epigenetic modification assay - An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. - Chris Stoeckert - Jie Zheng - Penn group + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. + Chris Stoeckert + Jie Zheng + Penn group epigenetic modification assay @@ -60501,10 +65431,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. NextSeq 500 - A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina NextSeq 500 - http://systems.illumina.com/systems/nextseq-sequencer.html + A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Illumina NextSeq 500 + http://systems.illumina.com/systems/nextseq-sequencer.html NextSeq 500 @@ -60522,10 +65452,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Illumina HiSeq 1000 - A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - HiSeq 1000 - http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + HiSeq 1000 + http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 1000 @@ -60543,12 +65473,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human Genome U133 Plus 2.0 tiling array - A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Affymetrix HT Human Genome U133 Plus 2 Array Plate Set - HG-U133 Plus 2 - HG-U133 Plus 2 array - http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 + A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Affymetrix HT Human Genome U133 Plus 2 Array Plate Set + HG-U133 Plus 2 + HG-U133 Plus 2 array + http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 Human Genome U133 Plus 2.0 tiling array @@ -60566,11 +65496,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. SOLiD 4 System - An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Applied Biosystems SOLiD 4 System - SOLiD 4 - http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 + An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Applied Biosystems SOLiD 4 System + SOLiD 4 + http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 SOLiD 4 System @@ -60588,12 +65518,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human Exon 1.0 ST tilling array - A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Affymetrix Human Exon 1.0 St Array - Human Exon 1.0 - Human Exon 1.0 ST Array - http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 + A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Affymetrix Human Exon 1.0 St Array + Human Exon 1.0 + Human Exon 1.0 ST Array + http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 Human Exon 1.0 ST tilling array @@ -60611,12 +65541,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human Genome U133 tiling array - A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Affymetrix HT Human Genome U133 Array Plate Set - HG-U133 - HG-U133 array - http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 + A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Affymetrix HT Human Genome U133 Array Plate Set + HG-U133 + HG-U133 array + http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 Human Genome U133 tiling array @@ -60628,11 +65558,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Genome Analyzer IIe - An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina GA IIe - Illumina Genome Analyzer IIe - http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Illumina GA IIe + Illumina Genome Analyzer IIe + http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf Genome Analyzer IIe @@ -60695,15 +65625,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. serial analysis of gene expression assay - PMID:15905473 - - A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. - Chris Stoeckert - Janos Demeter - Jie Zheng - SAGE - PMID:7570003 - https://sourceforge.net/p/obi/obi-terms/720/ + PMID:15905473 + + A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. + Chris Stoeckert + Janos Demeter + Jie Zheng + SAGE + PMID:7570003 + https://sourceforge.net/p/obi/obi-terms/720/ serial analysis of gene expression assay @@ -60738,15 +65668,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. genotyping by tiling array assay - PMID:19521816 - - A genotyping by array assay that uses tiling array technology. - Chris Stoeckert - Janos Demeter - Jie Zheng - DNA sequence variation detection by tiling array - PMID:19521816 - https://sourceforge.net/p/obi/obi-terms/720/ + PMID:19521816 + + A genotyping by array assay that uses tiling array technology. + Chris Stoeckert + Janos Demeter + Jie Zheng + DNA sequence variation detection by tiling array + PMID:19521816 + https://sourceforge.net/p/obi/obi-terms/720/ genotyping by tiling array assay @@ -60781,15 +65711,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. genotyping by SNP array assay - PMID:20080586 - - A genotyping by array assay that uses SNP array technology. - Chris Stoeckert - Janos Demeter - Jie Zheng - DNA sequence variation detection by snp array - PMID:20393561 - https://sourceforge.net/p/obi/obi-terms/720/ + PMID:20080586 + + A genotyping by array assay that uses SNP array technology. + Chris Stoeckert + Janos Demeter + Jie Zheng + DNA sequence variation detection by snp array + PMID:20393561 + https://sourceforge.net/p/obi/obi-terms/720/ genotyping by SNP array assay @@ -60858,14 +65788,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. parallel analysis of RNA structure assay - pmid:20811459 - - A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes - Chris Stoeckert - Janos Demeter - PARS - PMID:20811459 - https://sourceforge.net/p/obi/obi-terms/725/ + pmid:20811459 + + A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes + Chris Stoeckert + Janos Demeter + PARS + PMID:20811459 + https://sourceforge.net/p/obi/obi-terms/725/ parallel analysis of RNA structure assay @@ -60876,14 +65806,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. translation-associated transcript leader sequencing assay - pmid:23580730 - - An RNA-seq assay that combines TL-seq with polysome fractionation - Chris Stoeckert - Janos Demeter - TATL-seq - PMID:23580730 - https://sourceforge.net/p/obi/obi-terms/725/ + pmid:23580730 + + An RNA-seq assay that combines TL-seq with polysome fractionation + Chris Stoeckert + Janos Demeter + TATL-seq + PMID:23580730 + https://sourceforge.net/p/obi/obi-terms/725/ translation-associated transcript leader sequencing assay @@ -60894,14 +65824,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. transcript leader sequencing assay - pmid:23580730 - - An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. - Chris Stoeckert - Janos Demeter - TL-seq - PMID:23580730 - https://sourceforge.net/p/obi/obi-terms/725/ + pmid:23580730 + + An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. + Chris Stoeckert + Janos Demeter + TL-seq + PMID:23580730 + https://sourceforge.net/p/obi/obi-terms/725/ transcript leader sequencing assay @@ -60913,14 +65843,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. peptide mass fingerprinting assay - A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. - Chris Stoeckert - Janos Demeter - PMF - protein fingerprinting - ERO:0001668 - url:http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting - https://sourceforge.net/p/obi/obi-terms/725/ + A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. + Chris Stoeckert + Janos Demeter + PMF + protein fingerprinting + ERO:0001668 + url:http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting + https://sourceforge.net/p/obi/obi-terms/725/ peptide mass fingerprinting assay @@ -60931,13 +65861,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. array based nucleic acid structure mapping assay - pmid:23580730 + pmid:23580730 - An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. - Chris Stoeckert - Janos Demeter - OBI:0000870 - https://sourceforge.net/p/obi/obi-terms/725/ + An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. + Chris Stoeckert + Janos Demeter + OBI:0000870 + https://sourceforge.net/p/obi/obi-terms/725/ array based nucleic acid structure mapping assay @@ -60948,12 +65878,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. micrococcal nuclease digestion followed by tiling array assay - pmid:17873876 + pmid:17873876 - An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays - Chris Stoeckert - Janos Demeter - https://sourceforge.net/p/obi/obi-terms/725/ + An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays + Chris Stoeckert + Janos Demeter + https://sourceforge.net/p/obi/obi-terms/725/ micrococcal nuclease digestion followed by tiling array assay @@ -60964,16 +65894,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. ribosomal profiling by sequencing assay - Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 - - A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Ribo-seq - Ribo-seq assay - ribosomal profiling - PMID:24468696 + Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 + + A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Ribo-seq + Ribo-seq assay + ribosomal profiling + PMID:24468696 ribosomal profiling by sequencing assay @@ -60984,15 +65914,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. assay for transposase-accessible chromatin using sequencing - Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. - - An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. - Chris Stoeckert - Jie Zheng - Venkat Malladi - ATAC-seq - ATAC-seq assay - PMID:24097267 + Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. + + An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. + Chris Stoeckert + Jie Zheng + Venkat Malladi + ATAC-seq + ATAC-seq assay + PMID:24097267 assay for transposase-accessible chromatin using sequencing @@ -61009,16 +65939,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. chromatin isolation by RNA purification sequencing assay - Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. - - A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - ChIRP-seq - ChIRP-seq assay - Chromatin Isolation by RNA purification - PMID:21963238 + Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. + + A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + ChIRP-seq + ChIRP-seq assay + Chromatin Isolation by RNA purification + PMID:21963238 chromatin isolation by RNA purification sequencing assay @@ -61029,16 +65959,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. self-transcribing active regulatory region sequencing assay - Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. - - An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. - Chris Stoeckert - Jie Zheng - Venkat Malladi - STARR-seq - STARR-seq assay - self-transcribing active regulatory region sequencing - PMID:23328393 + Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. + + An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. + Chris Stoeckert + Jie Zheng + Venkat Malladi + STARR-seq + STARR-seq assay + self-transcribing active regulatory region sequencing + PMID:23328393 self-transcribing active regulatory region sequencing assay @@ -61049,16 +65979,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. carbon-copy chromosome conformation capture assay followed by sequencing assay - Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. - - A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Carbon-copy chromosome conformation capture assay followed by sequencing - HiC - HiC assay - PMID:19815776 + Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. + + A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Carbon-copy chromosome conformation capture assay followed by sequencing + HiC + HiC assay + PMID:19815776 carbon-copy chromosome conformation capture assay followed by sequencing assay @@ -61069,16 +65999,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay - Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 - - A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. - Chris Stoeckert - Jie Zheng - Venkat Malladi - iCLIP - iCLIP assay - individual-nucleotide resolution cross-linking and immunoprecipitation - doi:10.1016/j.ymeth.2013.10.011 + Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 + + A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. + Chris Stoeckert + Jie Zheng + Venkat Malladi + iCLIP + iCLIP assay + individual-nucleotide resolution cross-linking and immunoprecipitation + doi:10.1016/j.ymeth.2013.10.011 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay @@ -61090,14 +66020,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. RNA Bind-n-Seq assay - An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - RBNS - RNA Bind-n-Seq - RNBS assay - doi: 10.1016/j.molcel.2014.04.016 + An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + RBNS + RNA Bind-n-Seq + RNBS assay + doi: 10.1016/j.molcel.2014.04.016 RNA Bind-n-Seq assay @@ -61108,17 +66038,17 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. polyA-site sequencing assay - Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. - - A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. - Chris Stoeckert - Jie Zheng - Venkat Malladi - PAS-seq - PAS-seq assay - Poly(A)-site sequencing - poly(A)-site sequencing assay - doi: 10.1261/rna.2581711 + Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. + + A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. + Chris Stoeckert + Jie Zheng + Venkat Malladi + PAS-seq + PAS-seq assay + Poly(A)-site sequencing + poly(A)-site sequencing assay + doi: 10.1261/rna.2581711 polyA-site sequencing assay @@ -61140,16 +66070,16 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - surface plasmon resonance sensor chip - ProteOn GLC Sensor Chip #176-5011 + surface plasmon resonance sensor chip + ProteOn GLC Sensor Chip #176-5011 - A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached - Anna Maria Masci - SPR sensor chip - biosensor chip - sensor chip - OBI - surface plasmon resonance sensor chip + A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached + Anna Maria Masci + SPR sensor chip + biosensor chip + sensor chip + OBI + surface plasmon resonance sensor chip @@ -61201,10 +66131,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Illumina HiSeq 3000 - A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - PERSON: Sagar Jain, Richard Scheuermann - HiSeq 3000 - http://www.illumina.com/systems/hiseq-3000-4000.html + A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + PERSON: Sagar Jain, Richard Scheuermann + HiSeq 3000 + http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 3000 @@ -61222,10 +66152,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Illumina HiSeq 4000 - A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - PERSON: Sagar Jain, Richard Scheuermann - HiSeq 4000 - http://www.illumina.com/systems/hiseq-3000-4000.html + A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + PERSON: Sagar Jain, Richard Scheuermann + HiSeq 4000 + http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 4000 @@ -61237,27 +66167,32 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + - + + + + + + - - 3D structure determining assay of a MHC:ligand complex + + 3D molecular structure determination assay of a MHC:ligand complex - A MHC:ligand binding assay that uses a 3D structure determination of bound complex assay. - IEDB - IEDB - 3D structure|any method - 3D structure determining assay of a MHC:ligand complex + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex. + IEDB + IEDB + 3D structure|any method + 3D molecular structure determination assay of a MHC:ligand complex @@ -61290,10 +66225,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. - IEDB - IEDB - pathogen burden after challenge|in vivo assay + A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. + IEDB + IEDB + pathogen burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden @@ -61317,10 +66252,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vivo assay measuring B cell epitope specific protection from tumor challenge - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. - IEDB - IEDB - tumor burden after challenge|in vivo assay + A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. + IEDB + IEDB + tumor burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge @@ -61332,21 +66267,31 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + microarray assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a microarray. - IEDB - IEDB - qualitative binding|microarray + A microarray assay that detects the binding of an antigen with an antibody. + IEDB + IEDB + qualitative binding|microarray microarray assay measuring binding of a B cell epitope:antibody complex @@ -61363,6 +66308,19 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + @@ -61378,10 +66336,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. - IEDB - IEDB - dissociation constant KD|nuclear magnetic resonance (NMR)|nM + A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. + IEDB + IEDB + dissociation constant KD|nuclear magnetic resonance (NMR)|nM NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -61393,7 +66351,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -61411,14 +66369,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - assay measuring T cell epitope specific biological activity + + assay measuring biological activity resulting from T cell epitope:MHC:TCR binding - A T cell epitope recognition assay that detects biological activity. - IEDB - IEDB - biological activity|any method - assay measuring T cell epitope specific biological activity + A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope. + IEDB + IEDB + biological activity|any method + assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -61429,13 +66387,23 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + + + + @@ -61443,13 +66411,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells - A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. - IEDB - IEDB - CCL17/TARC release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells + A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. + IEDB + IEDB + CCL17/TARC release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells @@ -61460,13 +66428,23 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + + + + @@ -61474,13 +66452,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells + assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells - A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. - IEDB - IEDB - MIF release|biological activity - biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells + A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. + IEDB + IEDB + MIF release|biological activity + assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells @@ -61491,13 +66469,23 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + + + + @@ -61505,13 +66493,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - biological activity assay measuring epitope specific oncostatin M production by T cells + assay measuring epitope specific oncostatin M production by T cells - A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. - IEDB - IEDB - oncostatin M release|biological activity - biological activity assay measuring epitope specific oncostatin M production by T cells + A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. + IEDB + IEDB + oncostatin M release|biological activity + assay measuring epitope specific oncostatin M production by T cells @@ -61519,19 +66507,33 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + + + + + + + + + + + + + + + + + + + + + assay measuring a binding constant of a T cell epitope:MHC:TCR complex - A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. - IEDB - IEDB - binding constant|binding assay + A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. + IEDB + IEDB + binding constant|binding assay assay measuring a binding constant of a T cell epitope:MHC:TCR complex @@ -61543,21 +66545,37 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - CCL17/TARC release|RNA/DNA detection + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells. + IEDB + IEDB + CCL17/TARC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells @@ -61569,21 +66587,37 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - CCL22/MDC release|cytometric bead array + A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells. + IEDB + IEDB + CCL22/MDC release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells @@ -61606,10 +66640,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vitro assay measuring epitope specific T cell killing - A T cell epitope specific killing assay that uses an in vitro cell killing assay. - IEDB - IEDB - cytotoxicity|in vitro assay + A T cell epitope specific killing assay that uses an in vitro cell killing assay. + IEDB + IEDB + cytotoxicity|in vitro assay in vitro assay measuring epitope specific T cell killing @@ -61632,10 +66666,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. cytometric bead array assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay. - IEDB - IEDB - granzyme A release|cytometric bead array + A T cell epitope specific granzyme A release assay that uses a cytometric bead array assay. + IEDB + IEDB + granzyme A release|cytometric bead array cytometric bead array assay measuring epitope specific granzyme A release by T cells @@ -61658,10 +66692,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells - A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - granzyme A release|RNA/DNA detection + A T cell epitope specific granzyme A release assay that uses a detection of specific nucleic acids with complementary probes assay. + IEDB + IEDB + granzyme A release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells @@ -61684,10 +66718,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. cytometric bead array assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay. - IEDB - IEDB - granzyme B release|cytometric bead array + A T cell epitope specific granzyme B release assay that uses a cytometric bead array assay. + IEDB + IEDB + granzyme B release|cytometric bead array cytometric bead array assay measuring epitope specific granzyme B release by T cells @@ -61710,10 +66744,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells - A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay. - IEDB - IEDB - granzyme B release|RNA/DNA detection + A T cell epitope specific granzyme B release assay that uses a detection of specific nucleic acids with complementary probes assay. + IEDB + IEDB + granzyme B release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells @@ -61725,21 +66759,37 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells - An assay of epitope specific macrophage migration inhibitory factor (MIF) production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - MIF release|cytometric bead array + A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. + IEDB + IEDB + MIF release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells @@ -61751,21 +66801,37 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific oncostatin M production by T cells - An assay of epitope specific oncostatin M production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - oncostatin M release|cytometric bead array + A cytometric bead array assay that detects oncostatin M production by T cells. + IEDB + IEDB + oncostatin M release|cytometric bead array cytometric bead array assay measuring epitope specific oncostatin M production by T cells @@ -61788,10 +66854,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. ELISPOT assay measuring epitope specific perforin release by T cells - A T cell epitope specific perforin release assay that uses an ELISPOT assay. - IEDB - IEDB - perforin release|ELISPOT + A T cell epitope specific perforin release assay that uses an ELISPOT assay. + IEDB + IEDB + perforin release|ELISPOT ELISPOT assay measuring epitope specific perforin release by T cells @@ -61815,10 +66881,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vivo assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay that is performed in vivo. - IEDB - IEDB - proliferation|in vivo assay + A T cell epitope specific proliferation assay that is performed in vivo. + IEDB + IEDB + proliferation|in vivo assay in vivo assay measuring epitope specific proliferation of T cells @@ -61830,10 +66896,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vitro assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay that is performed on cells in vitro. - IEDB - IEDB - proliferation|in vitro assay + A T cell epitope specific proliferation assay that is performed on cells in vitro. + IEDB + IEDB + proliferation|in vitro assay in vitro assay measuring epitope specific proliferation of T cells @@ -61842,14 +66908,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + - assay measuring qualitiative binding of a MHC:ligand complex + assay measuring qualitative binding of a MHC:ligand complex - A MHC:ligand binding assay that detects qualitative binding. - IEDB - IEDB - qualitative binding|binding assay - assay measuring qualitiative binding of a MHC:ligand complex + An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output. + IEDB + IEDB + qualitative binding|binding assay + assay measuring qualitative binding of a MHC:ligand complex @@ -61871,10 +66957,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vivo assay measuring T cell epitope specific protection from challenge - An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. - IEDB - IEDB - protection from challenge|in vivo assay + An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. + IEDB + IEDB + protection from challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge @@ -61886,10 +66972,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. in vitro assay measuring T cell epitope specific suppression - T cell epitope dependent biological activity assay that detects suppression of an in vitro response. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - suppression|in vitro assay + T cell epitope dependent biological activity assay that detects suppression of an in vitro response. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + suppression|in vitro assay in vitro assay measuring T cell epitope specific suppression @@ -61901,13 +66987,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + + + + + + + + @@ -61917,10 +67010,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. MHC ligand assay - An immune epitope assay that detects either the processing and presentation of a ligand by an antigen presenting cell or the binding of a ligand to an MHC molecule. - IEDB - IEDB - ligand presentation/binding|binding assay + An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule. + IEDB + IEDB + MHC ligand assay|any method MHC ligand assay @@ -62058,12 +67151,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. reporter gene assay - An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. - Chris Stoeckert - Paul D. Thomas - reporter gene detection assay - Paul D. Thomas, Yang Chai; FaceBase - https://github.com/obi-ontology/obi/issues/781 + An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. + Chris Stoeckert + Paul D. Thomas + reporter gene detection assay + Paul D. Thomas, Yang Chai; FaceBase + https://github.com/obi-ontology/obi/issues/781 reporter gene assay @@ -62074,15 +67167,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. enhancer activity detection by reporter gene assay - PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" + PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" - A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. - Paul D. Thomas - Yang Chai - enhancer reporter gene assay - FaceBase - PMID 24614317 - https://github.com/obi-ontology/obi/issues/781 + A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. + Paul D. Thomas + Yang Chai + enhancer reporter gene assay + FaceBase + PMID 24614317 + https://github.com/obi-ontology/obi/issues/781 enhancer activity detection by reporter gene assay @@ -62093,14 +67186,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. transcription cofactor activity region identification by ChIP-Seq assay - PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" - - A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. - Paul D. Thomas - Yang Chai - chromatin modifier binding site identification by ChIP-Seq assay - PMID:19212405 - https://github.com/obi-ontology/obi/issues/782 + PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" + + A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. + Paul D. Thomas + Yang Chai + chromatin modifier binding site identification by ChIP-Seq assay + PMID:19212405 + https://github.com/obi-ontology/obi/issues/782 transcription cofactor activity region identification by ChIP-Seq assay @@ -62111,14 +67204,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. transcript expression location detection by hybridization chain reaction assay - PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" + PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" - An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. - Paul D. Thomas - Yang Chai - transcript expression location detection by fluorescent HCR. - PMID:21037591 - https://github.com/obi-ontology/obi/issues/783 + An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. + Paul D. Thomas + Yang Chai + transcript expression location detection by fluorescent HCR. + PMID:21037591 + https://github.com/obi-ontology/obi/issues/783 transcript expression location detection by hybridization chain reaction assay @@ -62130,15 +67223,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Tet-assisted bisulfite sequencing assay - A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. - Bjoern Peters - Chris Stoeckert - Jason Hilton - OBI - TAB-seq - Tet-assisted bisulfite sequencing - PMID:23196972 - http://sourceforge.net/p/obi/obi-terms/789/ + A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. + Bjoern Peters + Chris Stoeckert + Jason Hilton + OBI + TAB-seq + Tet-assisted bisulfite sequencing + PMID:23196972 + http://sourceforge.net/p/obi/obi-terms/789/ Tet-assisted bisulfite sequencing assay @@ -62175,14 +67268,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - specimen container - COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube + specimen container + COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube - A container with the function of containing a specimen. - For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ - Chris Stoeckert - Duke Biobank, OBIB - specimen container + A container with the function of containing a specimen. + For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ + Chris Stoeckert + Duke Biobank, OBIB + specimen container @@ -62203,14 +67296,14 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - physical store - a freezer. a humidity controlled box. + physical store + a freezer. a humidity controlled box. - A container with an environmental control function. - For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ - Chris Stoeckert - Duke Biobank, OBIB - physical store + A container with an environmental control function. + For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ + Chris Stoeckert + Duke Biobank, OBIB + physical store @@ -62288,15 +67381,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. MethylC-Capture sequencing assay - MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants. - - A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. - Chris Stoeckert - David Bujold - Capture Methylome - MCC-Seq - MethylC-Capture Sequencing - PMID:26021296 + MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants. + + A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. + Chris Stoeckert + David Bujold + Capture Methylome + MCC-Seq + MethylC-Capture Sequencing + PMID:26021296 MethylC-Capture sequencing assay @@ -62351,10 +67444,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay. - IEDB - IEDB - proliferation|CFSE + A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay. + IEDB + IEDB + proliferation|CFSE carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells @@ -62366,7 +67459,20 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + + + + + @@ -62382,10 +67488,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - A T cell epitope binding constant determination assay that measures the dissociation constant KD. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|binding assay|nM + A T cell epitope binding constant determination assay that measures the dissociation constant KD. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex @@ -62394,24 +67500,42 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex - A T cell epitope binding constant determination assay that measures the on rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|binding assay|M^-1s^-1 + A T cell epitope binding constant determination assay that measures the on rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|binding assay|M^-1s^-1 assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex @@ -62420,24 +67544,42 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex - A T cell epitope binding constant determination assay that measures the off rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|binding assay|1/s + A T cell epitope binding constant determination assay that measures the off rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|binding assay|1/s assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex @@ -62446,24 +67588,42 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex - A T cell epitope binding constant determination assay that measures the association constant KA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|binding assay|1/nM + A T cell epitope binding constant determination assay that measures the association constant KA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|binding assay|1/nM assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex @@ -62475,21 +67635,31 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - + + + + + + + + + + + + small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex - A B cell epitope 3D structure determination assay that uses a small-angle X-ray scattering assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|small-angle scattering assay + A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|small-angle scattering assay small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex @@ -62498,24 +67668,43 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex - A bio-layer interferometry assay that measures the on rate of a B cell epitope. - IEDB - IEDB - on rate|bio-layer interferometry assay|M^-1s^-1 + A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. + IEDB + IEDB + on rate|bio-layer interferometry assay|M^-1s^-1 bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex @@ -62524,24 +67713,43 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex - A bio-layer interferometry assay that measures the off rate of a B cell epitope. - IEDB - IEDB - off rate|bio-layer interferometry assay|1/s + A bio-layer interferometry assay that measures the off rate of an antigen with an antibody. + IEDB + IEDB + off rate|bio-layer interferometry assay|1/s bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex @@ -62550,13 +67758,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex - A bio-layer interferometry assay that detects a B cell epitope qualitative binding to antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|bio-layer interferometry assay + A bio-layer interferometry assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|bio-layer interferometry assay bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex @@ -62565,24 +67794,43 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A bio-layer interferometry assay that measures the dissociation constant [KD] of a B cell epitope binding. - IEDB - IEDB - dissociation constant KD|bio-layer interferometry assay|nM + A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. + IEDB + IEDB + dissociation constant KD|bio-layer interferometry assay|nM bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex @@ -62599,12 +67847,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. carboxyfluorescein succinimidyl ester staining assay - Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. + Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. - a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. - IEDB - CFSE assay - IEDB + a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. + IEDB + CFSE assay + IEDB carboxyfluorescein succinimidyl ester staining assay @@ -62615,12 +67863,12 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. bio-layer interferometry assay - Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds. + Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds. - A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. - IEDB - biolayer interferometry, BLI - IEDB + A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. + IEDB + biolayer interferometry, BLI + IEDB bio-layer interferometry assay @@ -62629,15 +67877,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - small-angle scattering assay - Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein + + small-angle scattering 3D molecular structure determination assay + Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein - A 3D structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. - IEDB - SAXS - IEDB - small-angle scattering assay + A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. + IEDB + SAXS + IEDB + small-angle scattering 3D molecular structure determination assay @@ -62654,11 +67902,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human 6x630K CGH Whole Genome Tiling Array - A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. - Term request: https://sourceforge.net/p/obi/obi-terms/791/ - Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group - NimbleGen Human 6x630K CGH Whole Genome Tiling Array - http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 + A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. + Term request: https://sourceforge.net/p/obi/obi-terms/791/ + Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group + NimbleGen Human 6x630K CGH Whole Genome Tiling Array + http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 Human 6x630K CGH Whole Genome Tiling Array @@ -62689,11 +67937,11 @@ https://www.doi.org/ enhanced cross-linking immunoprecipitation high-throughput sequencing assay - An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. - Chris Stoeckert - Jason Hilton - eCLIP - PMID:27018577 + An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. + Chris Stoeckert + Jason Hilton + eCLIP + PMID:27018577 enhanced cross-linking immunoprecipitation high-throughput sequencing assay @@ -62705,15 +67953,15 @@ https://www.doi.org/ small RNA sequencing assay - An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. - Chris Stoeckert - Jason Hilton - Mark A. Miller - short RNA-seq - small RNA-seq - url:http://science.sciencemag.org/content/316/5830/1484.full - url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html - https://github.com/obi-ontology/obi/issues/859 + An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. + Chris Stoeckert + Jason Hilton + Mark A. Miller + short RNA-seq + small RNA-seq + url:http://science.sciencemag.org/content/316/5830/1484.full + url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html + https://github.com/obi-ontology/obi/issues/859 small RNA sequencing assay @@ -62725,11 +67973,11 @@ https://www.doi.org/ bromouridine labeling and sequencing assay - An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. - Chris Stoeckert - Jason Hilton - Bru-seq - PMC:4009065 + An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. + Chris Stoeckert + Jason Hilton + Bru-seq + PMC:4009065 bromouridine labeling and sequencing assay @@ -62741,11 +67989,11 @@ https://www.doi.org/ bromouridine pulse-chase and sequencing assay - An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. - Chris Stoeckert - Jason Hilton - BruChase-seq - PMC:4009065 + An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. + Chris Stoeckert + Jason Hilton + BruChase-seq + PMC:4009065 bromouridine pulse-chase and sequencing assay @@ -62786,12 +68034,13 @@ https://www.doi.org/ cytometry time of flight assay - Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining refelctive of the level of expression of those surface receptors. + Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining refelctive of the level of expression of those surface receptors. - A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. - ImmPort - CyTOF - PMID:26190063 + A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. + ImmPort + CyTOF + mass cytometry assay + PMID:26190063 cytometry time of flight assay @@ -62831,12 +68080,12 @@ https://www.doi.org/ high performance liquid chromotography assay - On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. + On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. - An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. - ImmPort - HPLC - PMID:9491555 + An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. + ImmPort + HPLC + PMID:9491555 high performance liquid chromotography assay @@ -62847,14 +68096,14 @@ https://www.doi.org/ whole genome sequencing assay - WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. - - A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. - Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. - ImmPort - WGS - PMID:23095910 - PMID:25827230 + WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. + + A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + WGS + PMID:23095910 + PMID:25827230 whole genome sequencing assay @@ -62865,12 +68114,12 @@ https://www.doi.org/ exome sequencing assay - DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. + DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. - A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). - ImmPort - WES - PMID:25827230 + A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). + ImmPort + WES + PMID:25827230 exome sequencing assay @@ -62910,11 +68159,11 @@ https://www.doi.org/ microscopy assay - Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy. + Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy. - An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. - ImmPort - PMID:21685355 + An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. + ImmPort + PMID:21685355 microscopy assay @@ -62949,12 +68198,12 @@ https://www.doi.org/ mixed lymphocyte reaction assay - T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells. + T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells. - A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). - ImmPort - MLR - PMID:14969764 + A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). + ImmPort + MLR + PMID:14969764 mixed lymphocyte reaction assay @@ -62965,13 +68214,13 @@ https://www.doi.org/ killer cell immunoglobulin-like receptor typing assay - DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself. + DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself. - A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. - Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. - ImmPort - KIR typing - PMID:21239231 + A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + KIR typing + PMID:21239231 killer cell immunoglobulin-like receptor typing assay @@ -62982,14 +68231,14 @@ https://www.doi.org/ major histocompatibility typing assay - Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. - - A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. - Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. - IEDB - MHC typing, HLA typing - PMC:2628004 - PMID:27516207 + Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. + + A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + IEDB + MHC typing, HLA typing + PMC:2628004 + PMID:27516207 major histocompatibility typing assay @@ -63115,13 +68364,13 @@ https://www.doi.org/ - Illumina Genome Analyzer + Illumina Genome Analyzer - A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. - Person: Chris Stoeckert, Jason Hilton - Illumina Genome Analyzer I - http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html - Illumina Genome Analyzer + A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + Person: Chris Stoeckert, Jason Hilton + Illumina Genome Analyzer I + http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html + Illumina Genome Analyzer @@ -63130,13 +68379,13 @@ https://www.doi.org/ - Illumina HiSeq X Ten + Illumina HiSeq X Ten - A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann - HiSeq X Ten - http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html - Illumina HiSeq X Ten + A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann + HiSeq X Ten + http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html + Illumina HiSeq X Ten @@ -63145,12 +68394,12 @@ https://www.doi.org/ - Illumina Infinium Omni5Exome-4 Kit + Illumina Infinium Omni5Exome-4 Kit - An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. - Person: Chris Stoeckert, Jason Hilton - http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html - Illumina Infinium Omni5Exome-4 Kit + An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. + Person: Chris Stoeckert, Jason Hilton + http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html + Illumina Infinium Omni5Exome-4 Kit @@ -63159,12 +68408,12 @@ https://www.doi.org/ - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC BeadChip - An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. - Person: Chris Stoeckert, Jason Hilton - http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf - Illumina Infinium MethylationEPIC BeadChip + An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. + Person: Chris Stoeckert, Jason Hilton + http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf + Illumina Infinium MethylationEPIC BeadChip @@ -63175,13 +68424,13 @@ https://www.doi.org/ pulse stable isotope labeling by amino acids in cell culture - An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. - Rob Nash - dynamic SILAC - pulse SILAC - pulsed SILAC - PMID:18954100 - PMID:19053139 + An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. + Rob Nash + dynamic SILAC + pulse SILAC + pulsed SILAC + PMID:18954100 + PMID:19053139 pulse stable isotope labeling by amino acids in cell culture @@ -63193,21 +68442,37 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells - An assay of epitope specific chemokine (C-C motif) ligand 20 production by T cells that uses a cytometric bead array assay. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - CCL20/MIP-3a release|cytometric bead array + A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + CCL20/MIP-3a release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells @@ -63219,13 +68484,23 @@ https://www.doi.org/ - + - + + + + + + + + + + + @@ -63233,13 +68508,13 @@ https://www.doi.org/ - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - CCL20/MIP-3a release|biological activity - biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + CCL20/MIP-3a release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells @@ -63368,10 +68643,10 @@ https://www.doi.org/ temperature measurement assay - An assay to determine the temperature of an evaluant. - Bjoern Peters - Chris Stoeckert - OBI + An assay to determine the temperature of an evaluant. + Bjoern Peters + Chris Stoeckert + OBI temperature measurement assay @@ -63399,10 +68674,10 @@ https://www.doi.org/ volume measurement assay - An assay to determine the volume of an evaluant. - Bjoern Peters - Chris Stoeckert - OBI + An assay to determine the volume of an evaluant. + Bjoern Peters + Chris Stoeckert + OBI volume measurement assay @@ -63414,14 +68689,14 @@ https://www.doi.org/ Nanostring nCounter miRNA expression assay - A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. - Chris Stoeckert - Jason Hilton - microRNA counts - PMID:26729350 - url:http://www.nanostring.com/applications/technology - https://github.com/obi-ontology/obi/issues/806 - ENCODE DCC + A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. + Chris Stoeckert + Jason Hilton + microRNA counts + PMID:26729350 + url:http://www.nanostring.com/applications/technology + https://github.com/obi-ontology/obi/issues/806 + ENCODE DCC Nanostring nCounter miRNA expression assay @@ -63433,13 +68708,13 @@ https://www.doi.org/ bromouride labeling and sequencing after UV exposure - An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. - Chris Stoeckert - Jason Hilton - BruUV-seq - PMC:4675984 - https://github.com/obi-ontology/obi/issues/827 - ENCODE DCC + An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. + Chris Stoeckert + Jason Hilton + BruUV-seq + PMC:4675984 + https://github.com/obi-ontology/obi/issues/827 + ENCODE DCC bromouride labeling and sequencing after UV exposure @@ -63451,14 +68726,14 @@ https://www.doi.org/ extrachromosomal circular DNA sequencing assay - An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. - Chris Stoeckert - Jason Hilton - circulome-seq - eccDNA-seq - url:http://biorxiv.org/content/early/2017/04/19/128686 - https://github.com/obi-ontology/obi/issues/830 - ENCODE DCC + An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. + Chris Stoeckert + Jason Hilton + circulome-seq + eccDNA-seq + url:http://biorxiv.org/content/early/2017/04/19/128686 + https://github.com/obi-ontology/obi/issues/830 + ENCODE DCC extrachromosomal circular DNA sequencing assay @@ -63469,16 +68744,16 @@ https://www.doi.org/ antigen specific antibodies assay - Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens - - An analyte assay that measures the presence or amount of antibodies to a specified antigen. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens + + An analyte assay that measures the presence or amount of antibodies to a specified antigen. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB antigen specific antibodies assay @@ -63548,16 +68823,16 @@ https://www.doi.org/ HIV antibody assay - An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. - HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36) - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HIV I/II Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. + HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36) + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HIV I/II Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB HIV antibody assay @@ -63629,16 +68904,16 @@ https://www.doi.org/ HIV group O antibody assay - An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. - https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HIV I/II Plus O assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. + https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HIV I/II Plus O assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB HIV group O antibody assay @@ -63694,15 +68969,15 @@ https://www.doi.org/ surface HBV antibody assay - An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBsAb assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBsAb assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB surface HBV antibody assay @@ -63758,15 +69033,15 @@ https://www.doi.org/ core HBV antibody assay - An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBcAb assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBcAb assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB core HBV antibody assay @@ -63822,15 +69097,15 @@ https://www.doi.org/ core HBV IgM antibody assay - An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBcAb-IgM assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBcAb-IgM assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB core HBV IgM antibody assay @@ -63886,15 +69161,15 @@ https://www.doi.org/ HCV antibody assay - An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HCV Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HCV Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB HCV antibody assay @@ -63950,15 +69225,15 @@ https://www.doi.org/ EBV IgG antibody assay - An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - EBV IgG Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + EBV IgG Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB EBV IgG antibody assay @@ -64014,15 +69289,15 @@ https://www.doi.org/ EBV IgM antibody assay - An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - EBV IgM Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + EBV IgM Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB EBV IgM antibody assay @@ -64078,15 +69353,15 @@ https://www.doi.org/ CMV antibody assay - An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - CMV Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + CMV Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB CMV antibody assay @@ -64122,15 +69397,15 @@ https://www.doi.org/ venereal disease research laboratory test - An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - VDRL test - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + VDRL test + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB venereal disease research laboratory test @@ -64166,15 +69441,15 @@ https://www.doi.org/ rapid plasma reagin test - An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - RPR assay - url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + RPR assay + url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB rapid plasma reagin test @@ -64210,15 +69485,15 @@ https://www.doi.org/ HBV surface antigen assay - An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBsAg assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBsAg assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB HBV surface antigen assay @@ -64274,15 +69549,15 @@ https://www.doi.org/ HIV-1 nucleic acid testing - An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HIV-1 NAT - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HIV-1 NAT + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB HIV-1 nucleic acid testing @@ -64338,15 +69613,15 @@ https://www.doi.org/ HCV nucleic acid testing - An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HCV NAT - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB + An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HCV NAT + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB HCV nucleic acid testing @@ -64358,14 +69633,14 @@ https://www.doi.org/ multiplexed indexed T7 ChIP-seq assay - A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. - Chris Stoeckert - Jason Hilton - Mint-ChIP - Mint-ChIP-seq - url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 - https://github.com/obi-ontology/obi/issues/829 - ENCODE DCC + A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. + Chris Stoeckert + Jason Hilton + Mint-ChIP + Mint-ChIP-seq + url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 + https://github.com/obi-ontology/obi/issues/829 + ENCODE DCC multiplexed indexed T7 ChIP-seq assay @@ -64377,10 +69652,10 @@ https://www.doi.org/ systematic evolution of ligands by exponential enrichment assay - A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ - Rebecca Jackson - SELEX - PMID:21720957 + A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ + Rebecca Jackson + SELEX + PMID:21720957 systematic evolution of ligands by exponential enrichment assay @@ -64392,9 +69667,9 @@ https://www.doi.org/ footprinting assay - An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. - Bjoern Peters - doi:10.1002/3527600906.mcb.200300025 + An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. + Bjoern Peters + doi:10.1002/3527600906.mcb.200300025 footprinting assay @@ -64406,9 +69681,9 @@ https://www.doi.org/ DNAse footprinting assay - An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis - Rebecca Jackson - OBI development call + An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis + Rebecca Jackson + OBI development call DNAse footprinting assay @@ -64420,10 +69695,10 @@ https://www.doi.org/ mammalian 2-hybrid assay - A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. - Rebecca Jackson - ECO:0001095 - PMID:9043710 + A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. + Rebecca Jackson + ECO:0001095 + PMID:9043710 mammalian 2-hybrid assay @@ -64435,9 +69710,9 @@ https://www.doi.org/ protein localization assay - An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. - Rebecca Jackson - OBI development call + An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. + Rebecca Jackson + OBI development call protein localization assay @@ -64449,9 +69724,9 @@ https://www.doi.org/ tissue-based protein localization assay - A protein localization assay that determines the specific location of a protein in a living tissue sample. - Rebecca Jackson - PMID:14686950 + A protein localization assay that determines the specific location of a protein in a living tissue sample. + Rebecca Jackson + PMID:14686950 tissue-based protein localization assay @@ -64487,9 +69762,9 @@ https://www.doi.org/ subcellular protein localization assay - A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. - Rebecca Jackson - ECO + A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. + Rebecca Jackson + ECO subcellular protein localization assay @@ -64501,9 +69776,9 @@ https://www.doi.org/ subcellular protein immunohistochemistry assay - An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. - Rebecca Jackson - ECO + An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. + Rebecca Jackson + ECO subcellular protein immunohistochemistry assay @@ -64522,9 +69797,9 @@ https://www.doi.org/ ChIP-qPCR assay - A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. - Chris Stoeckert - PMID:18388953 + A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. + Chris Stoeckert + PMID:18388953 ChIP-qPCR assay @@ -64536,9 +69811,9 @@ https://www.doi.org/ genomic SELEX - A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. - Chris Stoeckert - PMID:20541015 + A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. + Chris Stoeckert + PMID:20541015 genomic SELEX @@ -64550,10 +69825,10 @@ https://www.doi.org/ dot blot assay - An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. - Bjoern Peters - dot blot analysis - PMID:10473518 + An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. + Bjoern Peters + dot blot analysis + PMID:10473518 dot blot assay @@ -64565,11 +69840,11 @@ https://www.doi.org/ Northwestern blot assay - A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. - Bjoern Peters - Northwestern analysis - Northwestern assay - PMID:26965261 + A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. + Bjoern Peters + Northwestern analysis + Northwestern assay + PMID:26965261 Northwestern blot assay @@ -64581,9 +69856,9 @@ https://www.doi.org/ Southwestern blot assay - A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. - Bjoern Peters - PMID:26404144 + A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. + Bjoern Peters + PMID:26404144 Southwestern blot assay @@ -64630,8 +69905,8 @@ https://www.doi.org/ immunocytochemistry - An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed - Bjoern Peters + An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed + Bjoern Peters immunocytochemistry @@ -64667,11 +69942,11 @@ https://www.doi.org/ ATP bioluminescence assay - An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. - Rebecca Jackson - ATP quantitation assay - cell viability ATP quantitation assay - ECO + An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. + Rebecca Jackson + ATP quantitation assay + cell viability ATP quantitation assay + ECO ATP bioluminescence assay @@ -64683,10 +69958,10 @@ https://www.doi.org/ electrophysiology assay - An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). - Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues. - Gully Burns - url:https://en.wikipedia.org/wiki/Electrophysiology + An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). + Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues. + Gully Burns + url:https://en.wikipedia.org/wiki/Electrophysiology electrophysiology assay @@ -64722,11 +69997,11 @@ https://www.doi.org/ patch clamp assay - An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. - Gully Burns - ECO:0006012 - url:http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 - url:https://en.wikipedia.org/wiki/Patch_clamp + An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. + Gully Burns + ECO:0006012 + url:http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 + url:https://en.wikipedia.org/wiki/Patch_clamp patch clamp assay @@ -64762,10 +70037,10 @@ https://www.doi.org/ whole-cell patch clamp assay - A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. - Gully Burns - ECO:0006015 - url:https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch + A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. + Gully Burns + ECO:0006015 + url:https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch whole-cell patch clamp assay @@ -64801,9 +70076,9 @@ https://www.doi.org/ cell-attached patch clamp assay - A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. - Gully Burns - url:https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch + A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. + Gully Burns + url:https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch cell-attached patch clamp assay @@ -64839,10 +70114,10 @@ https://www.doi.org/ inside-out patch clamp assay - A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. - Gully Burns - url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ - url:https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch + A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. + Gully Burns + url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ + url:https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch inside-out patch clamp assay @@ -64878,10 +70153,10 @@ https://www.doi.org/ outside-out patch clamp assay - A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. - Gully Burns - url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ - url:https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch + A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. + Gully Burns + url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ + url:https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch outside-out patch clamp assay @@ -64917,9 +70192,9 @@ https://www.doi.org/ voltage clamp assay - An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. - Gully Burns - url:https://en.wikipedia.org/wiki/Voltage_clamp + An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. + Gully Burns + url:https://en.wikipedia.org/wiki/Voltage_clamp voltage clamp assay @@ -64955,10 +70230,10 @@ https://www.doi.org/ two electrode voltage clamp assay - The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. - Gully Burns - TEVC - url:https://en.wikipedia.org/wiki/Voltage_clamp#Two-electrode_voltage_clamp_using_microelectrodes + The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. + Gully Burns + TEVC + url:https://en.wikipedia.org/wiki/Voltage_clamp#Two-electrode_voltage_clamp_using_microelectrodes two electrode voltage clamp assay @@ -64994,10 +70269,10 @@ https://www.doi.org/ cut open oocyte voltage clamp assay - The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. - Gully Burns - COVG - PMID:9711615 + The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. + Gully Burns + COVG + PMID:9711615 cut open oocyte voltage clamp assay @@ -65009,9 +70284,9 @@ https://www.doi.org/ current clamp assay - The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. - Gully Burns - url:https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp + The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. + Gully Burns + url:https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp current clamp assay @@ -65023,9 +70298,9 @@ https://www.doi.org/ electroencephalography - An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. - Gully Burns - EEG + An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. + Gully Burns + EEG electroencephalography @@ -65107,10 +70382,10 @@ https://www.doi.org/ single-unit recording - An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. - Can be used on any cell, not just neurons. - Gully Burns - url:http://www.thieme.com/media/samples/pubid-80418214.pdf + An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. + Can be used on any cell, not just neurons. + Gully Burns + url:http://www.thieme.com/media/samples/pubid-80418214.pdf single-unit recording @@ -65122,8 +70397,8 @@ https://www.doi.org/ multi-unit recording - An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. - Gully Burns + An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. + Gully Burns multi-unit recording @@ -65222,9 +70497,9 @@ https://www.doi.org/ local field potential recording - An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. - Gully Burns - doi:10.1007/978-1-4614-7320-6_723-1 + An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. + Gully Burns + doi:10.1007/978-1-4614-7320-6_723-1 local field potential recording @@ -65281,13 +70556,13 @@ https://www.doi.org/ - Leica Peloris rapid tissue processor + Leica Peloris rapid tissue processor - An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. - Chris Stoeckert, Helena Ellis - http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf - NCI BBRB - Leica Peloris rapid tissue processor + An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. + Chris Stoeckert, Helena Ellis + http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf + NCI BBRB + Leica Peloris rapid tissue processor @@ -65296,13 +70571,13 @@ https://www.doi.org/ - Microm Ergostar HM200 + Microm Ergostar HM200 - A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. - Chris Stoeckert, Helena Ellis - http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en - NCI BBRB - Microm Ergostar HM200 + A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. + Chris Stoeckert, Helena Ellis + http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en + NCI BBRB + Microm Ergostar HM200 @@ -65311,13 +70586,13 @@ https://www.doi.org/ - microtome blade + microtome blade - A device that is the part of a microtome used to slice specimens to a desired thickness. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Microtome - NCI BBRB - microtome blade + A device that is the part of a microtome used to slice specimens to a desired thickness. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Microtome + NCI BBRB + microtome blade @@ -65326,13 +70601,13 @@ https://www.doi.org/ - Sakura Low profile Accu-Edge microtome blade + Sakura Low profile Accu-Edge microtome blade - A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. - Chris Stoeckert, Helena Ellis - http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades - NCI BBRB - Sakura Low profile Accu-Edge microtome blade + A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. + Chris Stoeckert, Helena Ellis + http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades + NCI BBRB + Sakura Low profile Accu-Edge microtome blade @@ -65395,12 +70670,12 @@ https://www.doi.org/ reason for lack of data item - cannot be assessed, not applicable, unknown + cannot be assessed, not applicable, unknown - An information content entity that provides an explanation why a data item is not provided. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB + An information content entity that provides an explanation why a data item is not provided. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB reason for lack of data item @@ -65412,11 +70687,11 @@ https://www.doi.org/ cannot be assessed determination - A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. - Chris Stoeckert, Helena Ellis - cannot be assessed - OBI - NCI BBRB + A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. + Chris Stoeckert, Helena Ellis + cannot be assessed + OBI + NCI BBRB cannot be assessed determination @@ -65428,10 +70703,10 @@ https://www.doi.org/ determination if assay will provide reliable results - A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB + A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB determination if assay will provide reliable results @@ -65442,12 +70717,12 @@ https://www.doi.org/ GX - AJCC 7th edition GX: cannot be assessed. + AJCC 7th edition GX: cannot be assessed. - A cannot be assessed determination for histologic tumor grade. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB + A cannot be assessed determination for histologic tumor grade. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB GX @@ -65458,12 +70733,12 @@ https://www.doi.org/ pTX - AJCC 7th edition pTX: cannot be assessed. + AJCC 7th edition pTX: cannot be assessed. - A cannot be assessed determination for pathologic primary tumor staging. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB + A cannot be assessed determination for pathologic primary tumor staging. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB pTX @@ -65474,12 +70749,12 @@ https://www.doi.org/ pNX - AJCC 7th edition pNX: cannot be assessed. + AJCC 7th edition pNX: cannot be assessed. - A cannot be assessed determination of pathologic staging of lymph nodes. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB + A cannot be assessed determination of pathologic staging of lymph nodes. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB pNX @@ -65490,13 +70765,13 @@ https://www.doi.org/ histologic grade according to AJCC 7th edition - G4: Undifferentiated - G1:Well differentiated + G1:Well differentiated + G4: Undifferentiated - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB histologic grade according to AJCC 7th edition @@ -65508,11 +70783,11 @@ https://www.doi.org/ histologic grade according to the Fuhrman Nuclear Grading System - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. - Chris Stoeckert, Helena Ellis - Histologic Grade (Fuhrman Nuclear Grading System) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. + Chris Stoeckert, Helena Ellis + Histologic Grade (Fuhrman Nuclear Grading System) + NCI BBRB, OBI + NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System @@ -65524,10 +70799,10 @@ https://www.doi.org/ histologic grade for ovarian tumor - A categorical value specification that is a histologic grade assigned to a ovarian tumor. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a histologic grade assigned to a ovarian tumor. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB histologic grade for ovarian tumor @@ -65539,10 +70814,10 @@ https://www.doi.org/ histologic grade for ovarian tumor according to a two-tier grading system - A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system @@ -65554,10 +70829,10 @@ https://www.doi.org/ histologic grade for ovarian tumor according to the World Health Organization - A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB histologic grade for ovarian tumor according to the World Health Organization @@ -65569,11 +70844,11 @@ https://www.doi.org/ pathologic primary tumor stage for colon and rectum according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition @@ -65585,11 +70860,11 @@ https://www.doi.org/ pathologic primary tumor stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread lung primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread lung primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition @@ -65601,11 +70876,11 @@ https://www.doi.org/ pathologic primary tumor stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition @@ -65617,11 +70892,11 @@ https://www.doi.org/ pathologic primary tumor stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition @@ -65633,11 +70908,11 @@ https://www.doi.org/ pathologic lymph node stage for colon and rectum according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition @@ -65649,11 +70924,11 @@ https://www.doi.org/ pathologic lymph node stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition @@ -65665,11 +70940,11 @@ https://www.doi.org/ pathologic lymph node stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition @@ -65681,11 +70956,11 @@ https://www.doi.org/ pathologic lymph node stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition @@ -65697,11 +70972,11 @@ https://www.doi.org/ pathologic distant metastases stage for colon according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: colon distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: colon distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition @@ -65713,11 +70988,11 @@ https://www.doi.org/ pathologic distant metastases stage for lung according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: lung distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: lung distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition @@ -65729,11 +71004,11 @@ https://www.doi.org/ pathologic distant metastases stage for kidney according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: kidney distant Metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: kidney distant Metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition @@ -65745,11 +71020,11 @@ https://www.doi.org/ pathologic distant metastases stage for ovary according to AJCC 7th edition - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: ovarian distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: ovarian distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition @@ -65761,11 +71036,11 @@ https://www.doi.org/ clinical tumor stage group according to AJCC 7th edition - A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. - Chris Stoeckert, Helena Ellis - Clinical tumor stage group (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. + Chris Stoeckert, Helena Ellis + Clinical tumor stage group (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB clinical tumor stage group according to AJCC 7th edition @@ -65777,11 +71052,11 @@ https://www.doi.org/ International Federation of Gynecology and Obstetrics cervical cancer stage value specification - A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. - Chris Stoeckert, Helena Ellis - Clinical FIGO stage - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. + Chris Stoeckert, Helena Ellis + Clinical FIGO stage + NCI BBRB, OBI + NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification @@ -65793,11 +71068,11 @@ https://www.doi.org/ International Federation of Gynecology and Obstetrics ovarian cancer stage value specification - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. - Chris Stoeckert, Helena Ellis - Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) - NCI BBRB, OBI - NCI BBRB + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. + Chris Stoeckert, Helena Ellis + Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) + NCI BBRB, OBI + NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification @@ -65809,11 +71084,11 @@ https://www.doi.org/ performance status value specification - A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). - Chris Stoeckert, Helena Ellis - Performance Status Scale - https://en.wikipedia.org/wiki/Performance_status - NCI BBRB + A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + Chris Stoeckert, Helena Ellis + Performance Status Scale + https://en.wikipedia.org/wiki/Performance_status + NCI BBRB performance status value specification @@ -65825,11 +71100,11 @@ https://www.doi.org/ Eastern Cooperative Oncology Group score value specification - A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. - Chris Stoeckert, Helena Ellis - ECOG score - NCI BBRB, OBI - NCI BBRB + A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. + Chris Stoeckert, Helena Ellis + ECOG score + NCI BBRB, OBI + NCI BBRB Eastern Cooperative Oncology Group score value specification @@ -65841,11 +71116,11 @@ https://www.doi.org/ Karnofsky score vaue specification - A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. - Chris Stoeckert, Helena Ellis - Karnofsky Score - NCI BBRB, OBI - NCI BBRB + A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + Chris Stoeckert, Helena Ellis + Karnofsky Score + NCI BBRB, OBI + NCI BBRB Karnofsky score vaue specification @@ -65857,10 +71132,10 @@ https://www.doi.org/ clinical history of cancer - A clinical history in which there is a diagnosis of cancer. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB clinical history of cancer @@ -65872,11 +71147,11 @@ https://www.doi.org/ clinical history devoid of cancer - A clinical history in which there was no diagnosis of cancer. - Chris Stoeckert, Helena Ellis - clinical history of no cancer - NCI BBRB, OBIB - NCI BBRB + A clinical history in which there was no diagnosis of cancer. + Chris Stoeckert, Helena Ellis + clinical history of no cancer + NCI BBRB, OBIB + NCI BBRB clinical history devoid of cancer @@ -65888,10 +71163,10 @@ https://www.doi.org/ unknown clinical history of cancer - A clinical history in which it is not known whether there was a diagnosis of cancer. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which it is not known whether there was a diagnosis of cancer. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB unknown clinical history of cancer @@ -65903,11 +71178,11 @@ https://www.doi.org/ diagnosis of cancer - A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. - Chris Stoeckert, Helena Ellis - cancer diagnosis - OBIB - NCI BBRB + A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. + Chris Stoeckert, Helena Ellis + cancer diagnosis + OBIB + NCI BBRB diagnosis of cancer @@ -65919,11 +71194,11 @@ https://www.doi.org/ family clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a blood relative. - Chris Stoeckert, Helena Ellis - family history of cancer - NCI BBRB, OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a blood relative. + Chris Stoeckert, Helena Ellis + family history of cancer + NCI BBRB, OBIB + NCI BBRB family clinical history of cancer @@ -65935,10 +71210,10 @@ https://www.doi.org/ aunt clinical history of cancer - A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB aunt clinical history of cancer @@ -65950,10 +71225,10 @@ https://www.doi.org/ brother clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a male sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a male sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB brother clinical history of cancer @@ -65965,10 +71240,10 @@ https://www.doi.org/ daughter clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a person's female child. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a person's female child. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB daughter clinical history of cancer @@ -65980,10 +71255,10 @@ https://www.doi.org/ father clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a male parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a male parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB father clinical history of cancer @@ -65995,10 +71270,10 @@ https://www.doi.org/ mother clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a female parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a female parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB mother clinical history of cancer @@ -66010,10 +71285,10 @@ https://www.doi.org/ sister clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a female sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a female sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB sister clinical history of cancer @@ -66025,10 +71300,10 @@ https://www.doi.org/ son clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a person's male child. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a person's male child. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB son clinical history of cancer @@ -66040,10 +71315,10 @@ https://www.doi.org/ uncle clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB uncle clinical history of cancer @@ -66055,10 +71330,10 @@ https://www.doi.org/ grandmother clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a female parent of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a female parent of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB grandmother clinical history of cancer @@ -66070,10 +71345,10 @@ https://www.doi.org/ grandfather clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a male parent of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a male parent of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB grandfather clinical history of cancer @@ -66085,10 +71360,10 @@ https://www.doi.org/ nephew clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a male child of a sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a male child of a sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB nephew clinical history of cancer @@ -66100,10 +71375,10 @@ https://www.doi.org/ niece clinical history of cancer - A clinical history in which there is a diagnosis of cancer in a female child of a sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A clinical history in which there is a diagnosis of cancer in a female child of a sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB niece clinical history of cancer @@ -66115,10 +71390,10 @@ https://www.doi.org/ diagnosis of infectious disease - A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB diagnosis of infectious disease @@ -66130,10 +71405,10 @@ https://www.doi.org/ diagnosis of hepatitis B - A diagnosis of infectious disease caused by the hepatitis B virus. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A diagnosis of infectious disease caused by the hepatitis B virus. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB diagnosis of hepatitis B @@ -66145,10 +71420,10 @@ https://www.doi.org/ diagnosis of hepatitis C - A diagnosis of infectious disease caused by the hepatitis C virus. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A diagnosis of infectious disease caused by the hepatitis C virus. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB diagnosis of hepatitis C @@ -66160,10 +71435,10 @@ https://www.doi.org/ diagnosis of HIV - A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB diagnosis of HIV @@ -66175,10 +71450,10 @@ https://www.doi.org/ clinical history of repeated HIV assays - A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB clinical history of repeated HIV assays @@ -66190,10 +71465,10 @@ https://www.doi.org/ exposure to second hand smoke - A clinical history in which there has been second hand exposure to tobacco smoking. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which there has been second hand exposure to tobacco smoking. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB exposure to second hand smoke @@ -66205,10 +71480,10 @@ https://www.doi.org/ exposure to second hand smoke in household during childhood - An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB exposure to second hand smoke in household during childhood @@ -66220,10 +71495,10 @@ https://www.doi.org/ exposure to second hand smoke in current household - An exposure to second hand smoke in person's current household. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exposure to second hand smoke in person's current household. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB exposure to second hand smoke in current household @@ -66235,10 +71510,10 @@ https://www.doi.org/ pregnancy history - A clinical history in which a female has had a pregnancy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which a female has had a pregnancy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB pregnancy history @@ -66250,10 +71525,10 @@ https://www.doi.org/ number of pregnancies - A measurement datum of the total number of pregnancies a woman has had. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A measurement datum of the total number of pregnancies a woman has had. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB number of pregnancies @@ -66265,10 +71540,10 @@ https://www.doi.org/ number of live births - A measurement datum of the total number of live births a female has had. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A measurement datum of the total number of live births a female has had. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB number of live births @@ -66280,10 +71555,10 @@ https://www.doi.org/ age when gave birth to first child - An age measurement datum performed on a female when her first biological child was born. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An age measurement datum performed on a female when her first biological child was born. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB age when gave birth to first child @@ -66295,10 +71570,10 @@ https://www.doi.org/ gynecologic surgery history - A clinical history in which a woman has had gynecologic surgery in the past. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which a woman has had gynecologic surgery in the past. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB gynecologic surgery history @@ -66310,10 +71585,10 @@ https://www.doi.org/ hysterectomy history - A gynecologic surgery history in which a woman has had a hysterectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A gynecologic surgery history in which a woman has had a hysterectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB hysterectomy history @@ -66325,10 +71600,10 @@ https://www.doi.org/ unilateral oophorectomy history - A gynecologic surgery history in which a woman has had a unilateral oophorectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A gynecologic surgery history in which a woman has had a unilateral oophorectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB unilateral oophorectomy history @@ -66340,10 +71615,10 @@ https://www.doi.org/ neither hysterectomy nor oophorectomy history - A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB neither hysterectomy nor oophorectomy history @@ -66355,10 +71630,10 @@ https://www.doi.org/ hormonal birth control use history - An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB hormonal birth control use history @@ -66370,10 +71645,10 @@ https://www.doi.org/ hormonal birth control former use history - A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB hormonal birth control former use history @@ -66385,10 +71660,10 @@ https://www.doi.org/ hormonal birth control current use history - A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB hormonal birth control current use history @@ -66400,10 +71675,10 @@ https://www.doi.org/ no hormonal birth control use history - A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB no hormonal birth control use history @@ -66415,10 +71690,10 @@ https://www.doi.org/ hormonal replacement therapy history - A clinical history in which an individual has had hormonal replacement therapy in the past. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A clinical history in which an individual has had hormonal replacement therapy in the past. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB hormonal replacement therapy history @@ -66430,11 +71705,11 @@ https://www.doi.org/ delivery form for hormonal replacement therapy - A processed material used for delivery of hormones in hormone replacement therapy. - Chris Stoeckert, Helena Ellis - form of hormone replacement therapy - NCI BBRB, OBIB - NCI BBRB + A processed material used for delivery of hormones in hormone replacement therapy. + Chris Stoeckert, Helena Ellis + form of hormone replacement therapy + NCI BBRB, OBIB + NCI BBRB delivery form for hormonal replacement therapy @@ -66446,10 +71721,10 @@ https://www.doi.org/ pill delivery form for hormonal replacement therapy - A delivery form for hormonal replacement therapy that is a pill for oral administration. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A delivery form for hormonal replacement therapy that is a pill for oral administration. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB pill delivery form for hormonal replacement therapy @@ -66461,10 +71736,10 @@ https://www.doi.org/ patch delivery form for hormonal replacement therapy - A delivery form for hormonal replacement therapy that is a patch for transdermal administration. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A delivery form for hormonal replacement therapy that is a patch for transdermal administration. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB patch delivery form for hormonal replacement therapy @@ -66476,10 +71751,10 @@ https://www.doi.org/ cream delivery form for hormonal replacement therapy - A delivery form for hormonal replacement therapy that is a cream for transdermal administration. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A delivery form for hormonal replacement therapy that is a cream for transdermal administration. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB cream delivery form for hormonal replacement therapy @@ -66491,10 +71766,10 @@ https://www.doi.org/ menopausal status - An information content entity that indicates the state of a female's cessation of menstruation. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + An information content entity that indicates the state of a female's cessation of menstruation. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB menopausal status @@ -66506,10 +71781,10 @@ https://www.doi.org/ indeterminate menopausal status - A menopausal status that is neither pre- nor post-menopausal. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A menopausal status that is neither pre- nor post-menopausal. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB indeterminate menopausal status @@ -66521,10 +71796,10 @@ https://www.doi.org/ premenopausal status - A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB premenopausal status @@ -66536,10 +71811,10 @@ https://www.doi.org/ perimenopausal status - A menopausal status indicating that it has been 6-12 months since last menstrual period. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A menopausal status indicating that it has been 6-12 months since last menstrual period. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB perimenopausal status @@ -66551,10 +71826,10 @@ https://www.doi.org/ postmenopausal status - A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB postmenopausal status @@ -66566,10 +71841,10 @@ https://www.doi.org/ exposure to environmental and workplace carcinogens history - A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB exposure to environmental and workplace carcinogens history @@ -66581,10 +71856,10 @@ https://www.doi.org/ exposure to arsenic history - An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB exposure to arsenic history @@ -66596,10 +71871,10 @@ https://www.doi.org/ exposure to asbestos history - An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB exposure to asbestos history @@ -66611,10 +71886,10 @@ https://www.doi.org/ exposure to diesel exhaust history - An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB exposure to diesel exhaust history @@ -66626,10 +71901,10 @@ https://www.doi.org/ exposure to chromium history - An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB exposure to chromium history @@ -66641,10 +71916,10 @@ https://www.doi.org/ exposure to silica history - An exposure to environmental and workplace carcinogens history where the carcinogen is silica. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB + An exposure to environmental and workplace carcinogens history where the carcinogen is silica. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB exposure to silica history @@ -66656,11 +71931,11 @@ https://www.doi.org/ indicator of whether an inclusion criterion was met - An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process. - Chris Stoeckert, Helena Ellis - eligibility criterion met - NCI BBRB, OBIB - NCI BBRB + An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process. + Chris Stoeckert, Helena Ellis + eligibility criterion met + NCI BBRB, OBIB + NCI BBRB indicator of whether an inclusion criterion was met @@ -66672,11 +71947,11 @@ https://www.doi.org/ indicator of whether all inclusion criteria were met - An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process. - Chris Stoeckert, Helena Ellis - all eligibility criteria met - NCI BBRB, OBIB - NCI BBRB + An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process. + Chris Stoeckert, Helena Ellis + all eligibility criteria met + NCI BBRB, OBIB + NCI BBRB indicator of whether all inclusion criteria were met @@ -66688,10 +71963,10 @@ https://www.doi.org/ age of majority inclusion criterion - An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB age of majority inclusion criterion @@ -66703,10 +71978,10 @@ https://www.doi.org/ chemotherapy treatment exclusion criterion - An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB chemotherapy treatment exclusion criterion @@ -66718,10 +71993,10 @@ https://www.doi.org/ radiation treatment exclusion criteria - An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB radiation treatment exclusion criteria @@ -66732,12 +72007,12 @@ https://www.doi.org/ chemotherapy treatment within the recent past exclusion criterion - An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years. + An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years. - An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB chemotherapy treatment within the recent past exclusion criterion @@ -66748,12 +72023,12 @@ https://www.doi.org/ radiation treatment within the recent past exclusion criterion - An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years. + An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years. - An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB radiation treatment within the recent past exclusion criterion @@ -66764,12 +72039,12 @@ https://www.doi.org/ BMI range inclusion criterion - An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0 + An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0 - An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB BMI range inclusion criterion @@ -66780,12 +72055,12 @@ https://www.doi.org/ blood transfusion exclusion criterion - An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death. + An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death. - An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB blood transfusion exclusion criterion @@ -66797,10 +72072,10 @@ https://www.doi.org/ history of metastatic cancer exclusion criterion - An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB history of metastatic cancer exclusion criterion @@ -66811,12 +72086,12 @@ https://www.doi.org/ intravenous drug use exclusion criterion - Donor eligibility based on history of intravenous drug abuse in the last 5 years. + Donor eligibility based on history of intravenous drug abuse in the last 5 years. - An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB intravenous drug use exclusion criterion @@ -66827,12 +72102,12 @@ https://www.doi.org/ history of sex with someone with a history of blood borne infection exclusion criterion - Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years. + Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years. - An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB history of sex with someone with a history of blood borne infection exclusion criterion @@ -66843,12 +72118,12 @@ https://www.doi.org/ history of sex with someone with a history of intravenous drugs exclusion criterion - Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years. + Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years. - An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB history of sex with someone with a history of intravenous drugs exclusion criterion @@ -66860,10 +72135,10 @@ https://www.doi.org/ HIV exclusion criterion - An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB HIV exclusion criterion @@ -66874,12 +72149,12 @@ https://www.doi.org/ exposure to blood borne infectious disease exclusion criterion - Donor eligibility based on whether the donor has been exposed to HIV/AIDS. + Donor eligibility based on whether the donor has been exposed to HIV/AIDS. - An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB + An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB exposure to blood borne infectious disease exclusion criterion @@ -66897,9 +72172,9 @@ https://www.doi.org/ RNA interactome capture - An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. - Rebecca Jackson - PMID:26463381 + An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. + Rebecca Jackson + PMID:26463381 RNA interactome capture @@ -66909,14 +72184,14 @@ https://www.doi.org/ - widefield microscopy + widefield microscopy assay - A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. - Jie Zheng - WFM - url:http://bitesizebio.com/19409/the-many-flavors-of-widefield-microscopy/ - url:https://svi.nl/WideFieldMicroscope - widefield microscopy + A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. + Jie Zheng + WFM + url:http://bitesizebio.com/19409/the-many-flavors-of-widefield-microscopy/ + url:https://svi.nl/WideFieldMicroscope + widefield microscopy assay @@ -66939,9 +72214,9 @@ https://www.doi.org/ nuclear ligation assay - An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. - Chris S - PMID:8327891 + An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. + Chris S + PMID:8327891 nuclear ligation assay @@ -66959,11 +72234,11 @@ https://www.doi.org/ chromosome conformation capture assay - A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. - Chris S - 3C assay - PMID:11847345 - url:http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html + A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. + Chris S + 3C assay + PMID:11847345 + url:http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html chromosome conformation capture assay @@ -66975,9 +72250,9 @@ https://www.doi.org/ Hi-C assay - A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. - Chris S - PMID:20461051 + A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. + Chris S + PMID:20461051 Hi-C assay @@ -66989,7 +72264,7 @@ https://www.doi.org/ physical examination of individual - An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques. + An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques. physical examination of individual @@ -67059,9 +72334,9 @@ https://www.doi.org/ hydroxyl-radical footprinting assay - A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. - Jie Zheng - PMID:21770468 + A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. + Jie Zheng + PMID:21770468 hydroxyl-radical footprinting assay @@ -67137,11 +72412,11 @@ https://www.doi.org/ methidiumpropyl-EDTA-iron(II) footprinting assay - A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. - Jie Zheng - MPE-Fe(II) footprinting - PMID:6225070 - PMID:6435669 + A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. + Jie Zheng + MPE-Fe(II) footprinting + PMID:6225070 + PMID:6435669 methidiumpropyl-EDTA-iron(II) footprinting assay @@ -67203,10 +72478,10 @@ https://www.doi.org/ transcription start site mapping by primer extension assay - A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. - Rebecca Jackson - PMID:23378648 - url:https://en.wikipedia.org/wiki/Primer_extension + A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. + Rebecca Jackson + PMID:23378648 + url:https://en.wikipedia.org/wiki/Primer_extension transcription start site mapping by primer extension assay @@ -67218,9 +72493,9 @@ https://www.doi.org/ proteomic profiling design - A study design in which proteins in a sample are detected, quantified or otherwise analysed. - Dan Berrios - OBI:0001441 + A study design in which proteins in a sample are detected, quantified or otherwise analysed. + Dan Berrios + OBI:0001441 proteomic profiling design @@ -67232,11 +72507,11 @@ https://www.doi.org/ suppression subtractive hybridization - An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. - Rebecca Jackson - SSH - subtractive hybridization - PMID:14970460 + An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. + Rebecca Jackson + SSH + subtractive hybridization + PMID:14970460 suppression subtractive hybridization @@ -67248,11 +72523,11 @@ https://www.doi.org/ differential screening hybridization - An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. - Rebecca Jackson - DSH - differential screening - PMID:25472628 + An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. + Rebecca Jackson + DSH + differential screening + PMID:25472628 differential screening hybridization @@ -67261,19 +72536,34 @@ https://www.doi.org/ + + + + + + + + + + + + + + + + + + + + - - - - - - + footprinting assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a footprinting assay. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - qualitative binding|footprinting assay + A footprinting assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|footprinting assay footprinting assay measuring binding of a B cell epitope:antibody complex @@ -67285,21 +72575,31 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex - A footprinting assay that uses hydroxyl-radical footprinting to measure B cell epitope qualitative binding to antibody. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - qualitative binding|hydroxyl-radical footprinting assay + A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|hydroxyl-radical footprinting assay hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex @@ -67311,21 +72611,37 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-alpha production by T cells - An assay of epitope specific interferon-alpha production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNa release|ELISA + An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNa release|ELISA ELISA measuring epitope specific interferon-alpha production by T cells @@ -67337,13 +72653,23 @@ https://www.doi.org/ - + - + + + + + + + + + + + @@ -67351,13 +72677,13 @@ https://www.doi.org/ - biological activity assay measuring epitope specific interferon-alpha production by T cells + assay measuring epitope specific interferon-alpha production by T cells - A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNa release|biological activity - biological activity assay measuring epitope specific interferon-alpha production by T cells + A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNa release|biological activity + assay measuring epitope specific interferon-alpha production by T cells @@ -67435,12 +72761,12 @@ https://www.doi.org/ precision nuclear run-on sequencing assay - An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. - Rebecca Jackson - PRO-Seq - precision nuclear run-on and sequencing assay - PMID:23430654 - https://github.com/obi-ontology/obi/issues/876 + An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. + Rebecca Jackson + PRO-Seq + precision nuclear run-on and sequencing assay + PMID:23430654 + https://github.com/obi-ontology/obi/issues/876 precision nuclear run-on sequencing assay @@ -67459,12 +72785,12 @@ https://www.doi.org/ chromosome conformation capture-on-chip assay - A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. - Rebecca Jackson - 4C assay - circularized chromosome conformation capture assay - url:http://www.sciencedirect.com/science/article/pii/B9780123919380000045 - https://github.com/obi-ontology/obi/issues/875 + A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. + Rebecca Jackson + 4C assay + circularized chromosome conformation capture assay + url:http://www.sciencedirect.com/science/article/pii/B9780123919380000045 + https://github.com/obi-ontology/obi/issues/875 chromosome conformation capture-on-chip assay @@ -67482,12 +72808,12 @@ https://www.doi.org/ genotype phasing by Hi-C assay - A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. - Rebecca Jackson - haplotype reconstruction by Hi-C assay - PMID:19815776 - url:https://www.nature.com/articles/nbt.2728 - https://github.com/obi-ontology/obi/issues/828 + A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. + Rebecca Jackson + haplotype reconstruction by Hi-C assay + PMID:19815776 + url:https://www.nature.com/articles/nbt.2728 + https://github.com/obi-ontology/obi/issues/828 genotype phasing by Hi-C assay @@ -67864,12 +73190,12 @@ https://www.doi.org/ transcript analysis by single-end sequencing assay - A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. - Dan Berrios - Junhyong Kim - Stephen A. Fisher - transcript analysis by single-end sequencing - url:https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html + A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. + Dan Berrios + Junhyong Kim + Stephen A. Fisher + transcript analysis by single-end sequencing + url:https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html transcript analysis by single-end sequencing assay @@ -67893,12 +73219,12 @@ https://www.doi.org/ - microraft + microraft - A material separation device also commerically known as Isoraft, that is used to isolate single cells. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://en.wikipedia.org/wiki/Microrafts - microraft + A material separation device also commerically known as Isoraft, that is used to isolate single cells. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://en.wikipedia.org/wiki/Microrafts + microraft @@ -67907,12 +73233,12 @@ https://www.doi.org/ - pipette + pipette - A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://en.wikipedia.org/wiki/Pipette - pipette + A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://en.wikipedia.org/wiki/Pipette + pipette @@ -67975,10 +73301,10 @@ https://www.doi.org/ differential medium assay - an organism identification assay that uses a differential medium to achieve its objective - John Judkins - bacteriological assay - EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm + an organism identification assay that uses a differential medium to achieve its objective + John Judkins + bacteriological assay + EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm differential medium assay @@ -67990,11 +73316,11 @@ https://www.doi.org/ medication time value specification - A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material - John Judkins - medication timepoint - OBI - VEuPathDB + A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material + John Judkins + medication timepoint + OBI + VEuPathDB medication time value specification @@ -68006,11 +73332,11 @@ https://www.doi.org/ medication dose value specification - A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment - John Judkins - medication dose - OBI - VEuPathDB + A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment + John Judkins + medication dose + OBI + VEuPathDB medication dose value specification @@ -68069,9 +73395,9 @@ https://www.doi.org/ amniotic fluid specimen - A specimen that is derived from amniotic fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from amniotic fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank amniotic fluid specimen @@ -68102,9 +73428,9 @@ https://www.doi.org/ bile specimen - A specimen that is derived from bile. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from bile. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank bile specimen @@ -68135,9 +73461,9 @@ https://www.doi.org/ cerebrospinal fluid specimen - A specimen that is derived from cerbrospinal fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from cerbrospinal fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen @@ -68168,10 +73494,10 @@ https://www.doi.org/ feces specimen - A specimen that is derived from feces. - Chris Stoeckert - stool specimen - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from feces. + Chris Stoeckert + stool specimen + Chris Stoeckert, Penn Medicine Biobank feces specimen @@ -68202,10 +73528,10 @@ https://www.doi.org/ digestive system fluid or secretion specimen - A specimen that is derived from digestive system fluid or secretion. - Chris Stoeckert - gastric fluid specimen - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from digestive system fluid or secretion. + Chris Stoeckert + gastric fluid specimen + Chris Stoeckert, Penn Medicine Biobank digestive system fluid or secretion specimen @@ -68236,9 +73562,9 @@ https://www.doi.org/ milk specimen - A specimen that is derived from milk. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from milk. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank milk specimen @@ -68269,9 +73595,9 @@ https://www.doi.org/ pericardial fluid specimen - A specimen that is derived from pericardial fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from pericardial fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank pericardial fluid specimen @@ -68302,9 +73628,9 @@ https://www.doi.org/ saliva specimen - A specimen that is derived from saliva. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from saliva. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank saliva specimen @@ -68335,9 +73661,9 @@ https://www.doi.org/ sputum specimen - A specimen that is derived from sputum. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from sputum. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank sputum specimen @@ -68368,9 +73694,9 @@ https://www.doi.org/ sweat specimen - A specimen that is derived from sweat. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from sweat. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank sweat specimen @@ -68401,9 +73727,9 @@ https://www.doi.org/ synovial fluid specimen - A specimen that is derived from synovial fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from synovial fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank synovial fluid specimen @@ -68434,10 +73760,10 @@ https://www.doi.org/ vitreous humor specimen - A specimen that is derived from vireous humor. - Chris Stoeckert - vitreous fluid specimen - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from vireous humor. + Chris Stoeckert + vitreous fluid specimen + Chris Stoeckert, Penn Medicine Biobank vitreous humor specimen @@ -68468,9 +73794,9 @@ https://www.doi.org/ bone marrow specimen - A specimen that is derived from bone marrow. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from bone marrow. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank bone marrow specimen @@ -68501,9 +73827,9 @@ https://www.doi.org/ placenta specimen - A specimen that is derived from placenta. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from placenta. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank placenta specimen @@ -68534,9 +73860,9 @@ https://www.doi.org/ peritoneal fluid specimen - A specimen that is derived from peritoneal fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from peritoneal fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank peritoneal fluid specimen @@ -68567,9 +73893,9 @@ https://www.doi.org/ pleural fluid specimen - A specimen that is derived from pleural fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank + A specimen that is derived from pleural fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen @@ -68600,9 +73926,9 @@ https://www.doi.org/ brain specimen - A specimen that is derived from brain. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from brain. + Chris Stoeckert + Chris Stoeckert, NCI BBRB brain specimen @@ -68633,9 +73959,9 @@ https://www.doi.org/ hair specimen - A specimen that is derived from hair. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from hair. + Chris Stoeckert + Chris Stoeckert, NCI BBRB hair specimen @@ -68666,9 +73992,9 @@ https://www.doi.org/ prostate gland specimen - A specimen that is derived from prostate gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from prostate gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB prostate gland specimen @@ -68699,9 +74025,9 @@ https://www.doi.org/ skeletal muscle tissue specimen - A specimen that is derived from skeletal muscle. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from skeletal muscle. + Chris Stoeckert + Chris Stoeckert, NCI BBRB skeletal muscle tissue specimen @@ -68732,9 +74058,9 @@ https://www.doi.org/ heart specimen - A specimen that is derived from heart. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from heart. + Chris Stoeckert + Chris Stoeckert, NCI BBRB heart specimen @@ -68765,10 +74091,10 @@ https://www.doi.org/ renal medulla specimen - A specimen that is derived from renal medulla. - Chris Stoeckert - kidney medulla specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from renal medulla. + Chris Stoeckert + kidney medulla specimen + Chris Stoeckert, NCI BBRB renal medulla specimen @@ -68799,9 +74125,9 @@ https://www.doi.org/ adrenal gland specimen - A specimen that is derived from adrenal gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from adrenal gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB adrenal gland specimen @@ -68832,10 +74158,10 @@ https://www.doi.org/ breast specimen - A specimen that is derived from breast. - Chris Stoeckert - mammary tissue specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from breast. + Chris Stoeckert + mammary tissue specimen + Chris Stoeckert, NCI BBRB breast specimen @@ -68866,9 +74192,9 @@ https://www.doi.org/ urinary bladder specimen - A specimen that is derived from urinary bladder. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from urinary bladder. + Chris Stoeckert + Chris Stoeckert, NCI BBRB urinary bladder specimen @@ -68899,9 +74225,9 @@ https://www.doi.org/ tibial artery specimen - A specimen that is derived from tibial artery. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from tibial artery. + Chris Stoeckert + Chris Stoeckert, NCI BBRB tibial artery specimen @@ -68932,10 +74258,10 @@ https://www.doi.org/ skin of body specimen - A specimen that is derived from skin. - Chris Stoeckert - skin specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from skin. + Chris Stoeckert + skin specimen + Chris Stoeckert, NCI BBRB skin of body specimen @@ -68966,9 +74292,9 @@ https://www.doi.org/ pancreas specimen - A specimen that is derived from pancreas. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from pancreas. + Chris Stoeckert + Chris Stoeckert, NCI BBRB pancreas specimen @@ -68999,9 +74325,9 @@ https://www.doi.org/ stomach specimen - A specimen that is derived from stomach. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from stomach. + Chris Stoeckert + Chris Stoeckert, NCI BBRB stomach specimen @@ -69032,9 +74358,9 @@ https://www.doi.org/ pituitary gland specimen - A specimen that is derived from pituitary gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from pituitary gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB pituitary gland specimen @@ -69065,9 +74391,9 @@ https://www.doi.org/ adipose tissue specimen - A specimen that is derived from adipose tissue. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from adipose tissue. + Chris Stoeckert + Chris Stoeckert, NCI BBRB adipose tissue specimen @@ -69098,10 +74424,10 @@ https://www.doi.org/ cortex of kidney specimen - A specimen that is derived from cortex of kidney. - Chris Stoeckert - kidney cortex specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from cortex of kidney. + Chris Stoeckert + kidney cortex specimen + Chris Stoeckert, NCI BBRB cortex of kidney specimen @@ -69132,9 +74458,9 @@ https://www.doi.org/ esophagus mucosa specimen - A specimen that is derived from esophagus mucosa. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from esophagus mucosa. + Chris Stoeckert + Chris Stoeckert, NCI BBRB esophagus mucosa specimen @@ -69165,9 +74491,9 @@ https://www.doi.org/ colon specimen - A specimen that is derived from colon. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from colon. + Chris Stoeckert + Chris Stoeckert, NCI BBRB colon specimen @@ -69198,9 +74524,9 @@ https://www.doi.org/ lung specimen - A specimen that is derived from lung. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from lung. + Chris Stoeckert + Chris Stoeckert, NCI BBRB lung specimen @@ -69231,10 +74557,10 @@ https://www.doi.org/ esophagus muscularis mucosa specimen - A specimen that is derived from esophagus muscularis mucosa. - Chris Stoeckert - esophagus muscularis specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from esophagus muscularis mucosa. + Chris Stoeckert + esophagus muscularis specimen + Chris Stoeckert, NCI BBRB esophagus muscularis mucosa specimen @@ -69265,10 +74591,10 @@ https://www.doi.org/ cerebral cortex specimen - A specimen that is derived from cerebral cortex. - Chris Stoeckert - brain cortex specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from cerebral cortex. + Chris Stoeckert + brain cortex specimen + Chris Stoeckert, NCI BBRB cerebral cortex specimen @@ -69299,9 +74625,9 @@ https://www.doi.org/ thyroid gland specimen - A specimen that is derived from thyroid gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from thyroid gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB thyroid gland specimen @@ -69332,10 +74658,10 @@ https://www.doi.org/ cerebellum specimen - A specimen that is derived from cerebellum. - Chris Stoeckert - brain cerebellum specimen - Chris Stoeckert, NCI BBRB + A specimen that is derived from cerebellum. + Chris Stoeckert + brain cerebellum specimen + Chris Stoeckert, NCI BBRB cerebellum specimen @@ -69366,9 +74692,9 @@ https://www.doi.org/ tibial nerve specimen - A specimen that is derived from tibial nerve. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from tibial nerve. + Chris Stoeckert + Chris Stoeckert, NCI BBRB tibial nerve specimen @@ -69399,9 +74725,9 @@ https://www.doi.org/ coronary artery specimen - A specimen that is derived from coronary artery. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from coronary artery. + Chris Stoeckert + Chris Stoeckert, NCI BBRB coronary artery specimen @@ -69432,9 +74758,9 @@ https://www.doi.org/ spleen specimen - A specimen that is derived from spleen. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from spleen. + Chris Stoeckert + Chris Stoeckert, NCI BBRB spleen specimen @@ -69465,9 +74791,9 @@ https://www.doi.org/ aorta specimen - A specimen that is derived from aorta. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from aorta. + Chris Stoeckert + Chris Stoeckert, NCI BBRB aorta specimen @@ -69498,9 +74824,9 @@ https://www.doi.org/ atrial appendage specimen - A specimen that is derived from the atrium auricular region. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from the atrium auricular region. + Chris Stoeckert + Chris Stoeckert, NCI BBRB atrial appendage specimen @@ -69531,9 +74857,9 @@ https://www.doi.org/ esophagogastric junction specimen - A specimen that is derived from the esophagogastric junction. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from the esophagogastric junction. + Chris Stoeckert + Chris Stoeckert, NCI BBRB esophagogastric junction specimen @@ -69564,9 +74890,9 @@ https://www.doi.org/ ileum specimen - A specimen that is derived from ileum. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from ileum. + Chris Stoeckert + Chris Stoeckert, NCI BBRB ileum specimen @@ -69597,9 +74923,9 @@ https://www.doi.org/ liver specimen - A specimen that is derived from liver. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from liver. + Chris Stoeckert + Chris Stoeckert, NCI BBRB liver specimen @@ -69630,9 +74956,9 @@ https://www.doi.org/ minor salivary gland specimen - A specimen that is derived from minor salivary gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from minor salivary gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB minor salivary gland specimen @@ -69663,9 +74989,9 @@ https://www.doi.org/ omentum specimen - A specimen that is derived from omentum. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from omentum. + Chris Stoeckert + Chris Stoeckert, NCI BBRB omentum specimen @@ -69696,9 +75022,9 @@ https://www.doi.org/ ovary specimen - A specimen that is derived from female gonad. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from female gonad. + Chris Stoeckert + Chris Stoeckert, NCI BBRB ovary specimen @@ -69729,9 +75055,9 @@ https://www.doi.org/ sigmoid colon specimen - A specimen that is derived from sigmoid colon. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from sigmoid colon. + Chris Stoeckert + Chris Stoeckert, NCI BBRB sigmoid colon specimen @@ -69762,9 +75088,9 @@ https://www.doi.org/ suprapubic skin specimen - A specimen that is derived from suprapubic skin. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from suprapubic skin. + Chris Stoeckert + Chris Stoeckert, NCI BBRB suprapubic skin specimen @@ -69795,9 +75121,9 @@ https://www.doi.org/ testis specimen - A specimen that is derived from testis. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from testis. + Chris Stoeckert + Chris Stoeckert, NCI BBRB testis specimen @@ -69828,9 +75154,9 @@ https://www.doi.org/ uterus specimen - A specimen that is derived from uterus. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from uterus. + Chris Stoeckert + Chris Stoeckert, NCI BBRB uterus specimen @@ -69861,9 +75187,9 @@ https://www.doi.org/ vagina specimen - A specimen that is derived from vagina. - Chris Stoeckert - Chris Stoeckert, NCI BBRB + A specimen that is derived from vagina. + Chris Stoeckert + Chris Stoeckert, NCI BBRB vagina specimen @@ -70015,8 +75341,8 @@ https://www.doi.org/ histopathology assay - A histological assay that is intended to check for the presence or level of a specific disease. - OBI + A histological assay that is intended to check for the presence or level of a specific disease. + OBI histopathology assay @@ -70040,9 +75366,9 @@ https://www.doi.org/ adapter-sequence trimming - A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). - Dan Berrios - Dan Berrios + A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). + Dan Berrios + Dan Berrios adapter-sequence trimming @@ -70054,9 +75380,9 @@ https://www.doi.org/ file merge - A data transformation in which data contained in 2 or more files are merged into a single file. - Dan Berrios - Dan Berrios + A data transformation in which data contained in 2 or more files are merged into a single file. + Dan Berrios + Dan Berrios file merge @@ -70080,9 +75406,9 @@ https://www.doi.org/ sequence alignment - A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. - Dan Berrios - Dan Berrios + A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. + Dan Berrios + Dan Berrios sequence alignment @@ -70107,9 +75433,9 @@ https://www.doi.org/ sequence data feature count tabulation - The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. - Dan Berrios - Dan Berrios + The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. + Dan Berrios + Dan Berrios sequence data feature count tabulation @@ -70132,9 +75458,9 @@ https://www.doi.org/ trimmed sequence data - The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. - Dan Berrios - Dan Berrios + The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. + Dan Berrios + Dan Berrios trimmed sequence data @@ -70151,11 +75477,11 @@ https://www.doi.org/ nCounter Mouse miRNA Expression array - Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 - A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 - https://www.nanostring.com/products/mirna-assays/mirna-panels + A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 + https://www.nanostring.com/products/mirna-assays/mirna-panels nCounter Mouse miRNA Expression array @@ -70173,12 +75499,12 @@ https://www.doi.org/ polyA-selected RNA sequencing assay - An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. - Jason Hilton - Mark A. Miller - mRNA-seq - url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419 - ENCODE + An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. + Jason Hilton + Mark A. Miller + mRNA-seq + url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419 + ENCODE polyA-selected RNA sequencing assay @@ -70196,13 +75522,13 @@ https://www.doi.org/ polyA-depleted RNA sequencing assay - An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. - Jason Hilton - Mark A. Miller - polyA-depleted RNA-seq - url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733 - url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676 - ENCODE + An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. + Jason Hilton + Mark A. Miller + polyA-depleted RNA-seq + url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733 + url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676 + ENCODE polyA-depleted RNA sequencing assay @@ -70218,15 +75544,15 @@ https://www.doi.org/ - polyA depleted RNA extract + polyA depleted RNA extract - A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. - Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group + A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. + Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group 2018-05-11T16:35:11Z - polyA depleted RNA extract + polyA depleted RNA extract @@ -70235,13 +75561,13 @@ https://www.doi.org/ - RNA extraction with polyA depletion + RNA extraction with polyA depletion - A RNA extraction process in which only RNAs lacking a polyA tail are retained - Mark A. Miller, based on OBI_0000848 - UPenn Group + A RNA extraction process in which only RNAs lacking a polyA tail are retained + Mark A. Miller, based on OBI_0000848 + UPenn Group 2018-05-11T15:01:14Z - RNA extraction with polyA depletion + RNA extraction with polyA depletion @@ -70251,11 +75577,11 @@ https://www.doi.org/ isoform sequencing - Novel transcript forms were assessed by isoform sequencing. + Novel transcript forms were assessed by isoform sequencing. - A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. - ISO-seq - url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ + A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. + ISO-seq + url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ isoform sequencing @@ -70267,9 +75593,9 @@ https://www.doi.org/ adapter sequence data - Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. - Dan Berrios - Dan Berrios + Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. + Dan Berrios + Dan Berrios adapter sequence data @@ -70281,9 +75607,9 @@ https://www.doi.org/ adapter-trimmed sequence data - The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. - Dan Berrios - Dan Berrios + The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. + Dan Berrios + Dan Berrios adapter-trimmed sequence data @@ -70295,9 +75621,9 @@ https://www.doi.org/ aligned sequence data - The results of a sequence alignment. - Dan Berrios - Dan Berrios + The results of a sequence alignment. + Dan Berrios + Dan Berrios aligned sequence data @@ -70315,9 +75641,9 @@ https://www.doi.org/ merged aligned sequence data - The results of a data transformation of sequence data in which files containing aligned sequence data are merged together - Dan Berrios - Dan Berrios + The results of a data transformation of sequence data in which files containing aligned sequence data are merged together + Dan Berrios + Dan Berrios merged aligned sequence data @@ -70329,9 +75655,9 @@ https://www.doi.org/ sequence library feature count data - The results of a sequence data feature count tabulation. - Dan Berrios - Dan Berrios + The results of a sequence data feature count tabulation. + Dan Berrios + Dan Berrios sequence library feature count data @@ -70349,7 +75675,7 @@ https://www.doi.org/ DNA methylation profiling data - The results of a DNA methylation profiling assay + The results of a DNA methylation profiling assay DNA methylation profiling data @@ -70361,7 +75687,7 @@ https://www.doi.org/ differential expression analysis data - The results of a differential expression analysis. + The results of a differential expression analysis. differential expression analysis data @@ -70373,7 +75699,7 @@ https://www.doi.org/ sequence trimming - A data transformation in which subsequences of a molecular sequence are cut (removed). + A data transformation in which subsequences of a molecular sequence are cut (removed). sequence trimming @@ -70389,14 +75715,14 @@ https://www.doi.org/ - digital acquisition card + digital acquisition card - The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). - Mark A. Miller - DAQ device - digital acquisition and digital generation card - Brenda Farrell, bfarrell@bcm.edu - digital acquisition card + The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). + Mark A. Miller + DAQ device + digital acquisition and digital generation card + Brenda Farrell, bfarrell@bcm.edu + digital acquisition card @@ -70407,9 +75733,9 @@ https://www.doi.org/ machine learning - A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. + A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. Mark A. Miller - https://en.wikipedia.org/wiki/Machine_learning + https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN machine learning @@ -70422,9 +75748,9 @@ https://www.doi.org/ supervised machine learning - A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples. + A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples. Mark A. Miller - https://en.wikipedia.org/wiki/Supervised_learning + https://en.wikipedia.org/wiki/Supervised_learning https://github.com/TrisSN supervised machine learning @@ -70437,9 +75763,9 @@ https://www.doi.org/ unsupervised machine learning - A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized). + A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized). Mark A. Miller - https://en.wikipedia.org/wiki/Unsupervised_learning + https://en.wikipedia.org/wiki/Unsupervised_learning https://github.com/TrisSN unsupervised machine learning @@ -70458,9 +75784,9 @@ https://www.doi.org/ molecular interaction identification design - A study design that investigates the features of interaction between molecules. - Rebecca Jackson - person:RCT + A study design that investigates the features of interaction between molecules. + Rebecca Jackson + person:RCT molecular interaction identification design @@ -70472,9 +75798,9 @@ https://www.doi.org/ colocalization identification design - A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. - Rebecca Jackson - url:https://en.wikipedia.org/wiki/Colocalization + A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. + Rebecca Jackson + url:https://en.wikipedia.org/wiki/Colocalization colocalization identification design @@ -70502,9 +75828,9 @@ https://www.doi.org/ genetic interaction identification design - A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone. - Rebecca Jackson - MI:0208 + A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone. + Rebecca Jackson + MI:0208 genetic interaction identification design @@ -70516,9 +75842,9 @@ https://www.doi.org/ functional association identification design - A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other. - Rebecca Jackson - MI:2286 + A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other. + Rebecca Jackson + MI:2286 functional association identification design @@ -70546,10 +75872,10 @@ https://www.doi.org/ direct interaction identification design - A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. - Rebecca Jackson - molecular binding identification design - MI:0407 + A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. + Rebecca Jackson + molecular binding identification design + MI:0407 direct interaction identification design @@ -70561,9 +75887,9 @@ https://www.doi.org/ enzymatic reaction identification design - A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. - Rebecca Jackson - MI:0414 + A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. + Rebecca Jackson + MI:0414 enzymatic reaction identification design @@ -70575,9 +75901,9 @@ https://www.doi.org/ self interaction identification design - A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. - Rebecca Jackson - MI:1126 + A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. + Rebecca Jackson + MI:1126 self interaction identification design @@ -70665,11 +75991,11 @@ https://www.doi.org/ chromosome conformation capture sequencing assay - A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. - Rebecca Jackson - 3C-seq assay - PMID:23411633 - https://github.com/obi-ontology/obi/issues/939 + A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. + Rebecca Jackson + 3C-seq assay + PMID:23411633 + https://github.com/obi-ontology/obi/issues/939 chromosome conformation capture sequencing assay @@ -70681,10 +76007,10 @@ https://www.doi.org/ inverse polymerase chain reaction - A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR. - Rebecca Tauber - inverse PCR - url:https://en.wikipedia.org/wiki/Chromosome_conformation_capture + A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR. + Rebecca Tauber + inverse PCR + url:https://en.wikipedia.org/wiki/Chromosome_conformation_capture inverse polymerase chain reaction @@ -70734,9 +76060,9 @@ https://www.doi.org/ demultiplexed sequence data - Sequence data in which an identifier subsequence has been used to categorize each reads by source. - Dan Berrios - Dan Berrios + Sequence data in which an identifier subsequence has been used to categorize each reads by source. + Dan Berrios + Dan Berrios demultiplexed sequence data @@ -70748,9 +76074,9 @@ https://www.doi.org/ multiplexed sequence data - Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. - Dan Berrios - Dan Berrios + Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. + Dan Berrios + Dan Berrios multiplexed sequence data @@ -70787,9 +76113,9 @@ https://www.doi.org/ areolar swab specimen - A specimen that is collected with a swab from the surface of an areola of a breast. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of an areola of a breast. + Chris Stoeckert + Chris Stoeckert, OBIB areolar swab specimen @@ -70826,9 +76152,9 @@ https://www.doi.org/ breast swab specimen - A specimen that is collected with a swab from the surface of a breast. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a breast. + Chris Stoeckert + Chris Stoeckert, OBIB breast swab specimen @@ -70865,9 +76191,9 @@ https://www.doi.org/ cheek swab specimen - A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. + Chris Stoeckert + Chris Stoeckert, OBIB cheek swab specimen @@ -70904,9 +76230,9 @@ https://www.doi.org/ nasopharyngeal swab specimen - A specimen that is collected with a swab from the surface of a nasopharynx. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a nasopharynx. + Chris Stoeckert + Chris Stoeckert, OBIB nasopharyngeal swab specimen @@ -70943,9 +76269,9 @@ https://www.doi.org/ oral swab specimen - A specimen that is collected with a swab from the inside surface of a mouth. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the inside surface of a mouth. + Chris Stoeckert + Chris Stoeckert, OBIB oral swab specimen @@ -70982,9 +76308,9 @@ https://www.doi.org/ oropharyngeal swab specimen - A specimen that is collected with a swab from the surface of a oropharynx. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a oropharynx. + Chris Stoeckert + Chris Stoeckert, OBIB oropharyngeal swab specimen @@ -71021,9 +76347,9 @@ https://www.doi.org/ rectal swab specimen - A specimen that is collected with a swab from the surface of a rectum. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a rectum. + Chris Stoeckert + Chris Stoeckert, OBIB rectal swab specimen @@ -71060,9 +76386,9 @@ https://www.doi.org/ tongue swab specimen - A specimen that is collected with a swab from the surface of a tongue. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a tongue. + Chris Stoeckert + Chris Stoeckert, OBIB tongue swab specimen @@ -71099,9 +76425,9 @@ https://www.doi.org/ vagina swab specimen - A specimen that is collected with a swab from the surface of a vagina. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a vagina. + Chris Stoeckert + Chris Stoeckert, OBIB vagina swab specimen @@ -71138,10 +76464,10 @@ https://www.doi.org/ fecal swab specimen - A specimen that is collected with a swab from the surface of a feces. - Chris Stoeckert - stool swab specimen - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of a feces. + Chris Stoeckert + stool swab specimen + Chris Stoeckert, OBIB fecal swab specimen @@ -71178,9 +76504,9 @@ https://www.doi.org/ environmental swab specimen - A specimen that is collected with a swab from the surface of an environmenal material. - Chris Stoeckert - Chris Stoeckert, OBIB + A specimen that is collected with a swab from the surface of an environmenal material. + Chris Stoeckert + Chris Stoeckert, OBIB environmental swab specimen @@ -71191,11 +76517,11 @@ https://www.doi.org/ birth cohort study design - The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases. + The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases. - A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up. - MIABIS - MIABIS contributors + A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up. + MIABIS + MIABIS contributors birth cohort study design @@ -71206,11 +76532,11 @@ https://www.doi.org/ disease specific study design - A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design. + A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design. - A study design for which material and information is collected from subjects that have already developed a particular disease. - MIABIS - MIABIS contributors + A study design for which material and information is collected from subjects that have already developed a particular disease. + MIABIS + MIABIS contributors disease specific study design @@ -71221,11 +76547,11 @@ https://www.doi.org/ genealogical record - A family tree is a type of genealogical record. + A family tree is a type of genealogical record. - A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption. - MIABIS - Sarah Bost + A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption. + MIABIS + Sarah Bost genealogical record @@ -71236,12 +76562,12 @@ https://www.doi.org/ national registry - The Social Security Administration's Death Master File is a national registry in the United States. + The Social Security Administration's Death Master File is a national registry in the United States. - An information content entity that contains information about a nationwide group of individuals. - MIABIS - Sarah Bost - MIABIS contributors + An information content entity that contains information about a nationwide group of individuals. + MIABIS + Sarah Bost + MIABIS contributors national registry @@ -71252,12 +76578,12 @@ https://www.doi.org/ national biomedical registry - The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry. + The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry. - A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes. - MIABIS - Sarah Bost - MIABIS contributors + A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes. + MIABIS + Sarah Bost + MIABIS contributors national biomedical registry @@ -71330,13 +76656,13 @@ https://www.doi.org/ reconstitution assay - "In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313) + "In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313) - An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. - Rebecca Jackson - reconstitution experiment - url:https://jcs.biologists.org/content/132/4/jcs227488 - https://github.com/obi-ontology/obi/issues/1059 + An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. + Rebecca Jackson + reconstitution experiment + url:https://jcs.biologists.org/content/132/4/jcs227488 + https://github.com/obi-ontology/obi/issues/1059 reconstitution assay @@ -71358,12 +76684,12 @@ https://www.doi.org/ in vitro transcription reconstitution assay - An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214) + An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214) - A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. - Rebecca Jackson - PMID:9237163 - https://github.com/obi-ontology/obi/issues/1059 + A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. + Rebecca Jackson + PMID:9237163 + https://github.com/obi-ontology/obi/issues/1059 in vitro transcription reconstitution assay @@ -71375,13 +76701,13 @@ https://www.doi.org/ whole metagenome sequencing assay - A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. - Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). - Rebecca Jackson - WMS - Bjoern Peters - Michelle Giglio - https://github.com/obi-ontology/obi/issues/1056 + A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). + Rebecca Jackson + WMS + Bjoern Peters + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1056 whole metagenome sequencing assay @@ -71393,9 +76719,9 @@ https://www.doi.org/ case-control study design - A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. - John Judkins, Bjoern Peters - Wikipedia, OBI + A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. + John Judkins, Bjoern Peters + Wikipedia, OBI case-control study design @@ -71441,13 +76767,13 @@ https://www.doi.org/ - ribosomal RNA-depleted RNA extract - Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. + ribosomal RNA-depleted RNA extract + Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. - An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). - Dan Berrios + An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). + Dan Berrios https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 - ribosomal RNA-depleted RNA extract + ribosomal RNA-depleted RNA extract @@ -71463,14 +76789,14 @@ https://www.doi.org/ RNAi knockdown assay - "Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251) + "Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251) - A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. - Rebecca Jackson - RNA interference knockdown assay - RNAi gene knockdown assay - Rebecca Jackson - https://github.com/obi-ontology/obi/issues/1057 + A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. + Rebecca Jackson + RNA interference knockdown assay + RNAi gene knockdown assay + Rebecca Jackson + https://github.com/obi-ontology/obi/issues/1057 RNAi knockdown assay @@ -71479,16 +76805,16 @@ https://www.doi.org/ - + direct RNA sequencing assay - An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. - Dan Berrios - DRS - direct RNA-seq - url:https://www.nature.com/articles/nature08390 - https://github.com/obi-ontology/obi/issues/874 - jahilton + An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. + Dan Berrios + DRS + direct RNA-seq + url:https://www.nature.com/articles/nature08390 + https://github.com/obi-ontology/obi/issues/874 + jahilton direct RNA sequencing assay @@ -71504,14 +76830,14 @@ https://www.doi.org/ - Illumina NovaSeq 6000 - Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. + Illumina NovaSeq 6000 + Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - Dan Berrios - NovaSeq 6000 - http://www.illumina.com/systems/sequencing-platforms/novaseq.html - Illumina NovaSeq 6000 + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + Dan Berrios + NovaSeq 6000 + http://www.illumina.com/systems/sequencing-platforms/novaseq.html + Illumina NovaSeq 6000 @@ -71521,12 +76847,12 @@ https://www.doi.org/ single-cell RNA sequencing assay - Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells. + Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells. - An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. - Dan Berrios - scRNA-seq - Anna Maria Masci + An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. + Dan Berrios + scRNA-seq + Anna Maria Masci single-cell RNA sequencing assay @@ -71536,15 +76862,15 @@ https://www.doi.org/ - PacBio Sequel - The cDNAs were sequenced on the PacBio Sequel platform. + PacBio Sequel + The cDNAs were sequenced on the PacBio Sequel platform. - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - Bonita Lam - Dan Berrios - Pacific BioSciences Sequel - http://www.pacb.com/products-and-services/pacbio-systems/sequel/ - PacBio Sequel + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + Bonita Lam + Dan Berrios + Pacific BioSciences Sequel + http://www.pacb.com/products-and-services/pacbio-systems/sequel/ + PacBio Sequel @@ -71553,15 +76879,15 @@ https://www.doi.org/ - PacBio Sequel II - The cDNAs were sequenced on the PacBio Sequel II platform. + PacBio Sequel II + The cDNAs were sequenced on the PacBio Sequel II platform. - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. - Bonita Lam - Dan Berrios - Pacific BioSciences Sequel II - http://www.pacb.com/products-and-services/pacbio-systems/sequel/ - PacBio Sequel II + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + Bonita Lam + Dan Berrios + Pacific BioSciences Sequel II + http://www.pacb.com/products-and-services/pacbio-systems/sequel/ + PacBio Sequel II @@ -71584,10 +76910,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells - An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - disease exacerbation after adoptive transfer|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + disease exacerbation after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells @@ -71611,10 +76937,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells - An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - decreased disease after adoptive transfer|in vivo assay + An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + decreased disease after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells @@ -71638,10 +76964,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells - An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - decreased disease after adoptive transfer|in vivo assay + An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + decreased disease after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells @@ -71665,10 +76991,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells - An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - protection from challenge after adoptive transfer|in vivo assay + An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + protection from challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells @@ -71692,10 +77018,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - protection from challenge after adoptive transfer|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells @@ -71707,10 +77033,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - pathogen burden after challenge after adoptive transfer|in vivo assay + A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + pathogen burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden @@ -71722,10 +77048,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - pathogen burden after challenge after adoptive transfer|in vivo assay + A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + pathogen burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden @@ -71749,10 +77075,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - survival from challenge after adoptive transfer|in vivo assay + A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + survival from challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival @@ -71775,10 +77101,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - survival from challenge after adoptive transfer|in vivo assay + A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + survival from challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival @@ -71790,10 +77116,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - tumor burden after challenge after adoptive transfer|in vivo assay + A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + tumor burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells @@ -71805,10 +77131,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - tumor burden after challenge after adoptive transfer|in vivo assay + A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + tumor burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells @@ -71831,10 +77157,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells - An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - tolerance after adoptive transfer|in vivo assay + An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + tolerance after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells @@ -71857,10 +77183,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells - An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - tolerance after adoptive transfer|in vivo assay + An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + tolerance after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells @@ -71935,13 +77261,13 @@ https://www.doi.org/ Giemsa stain assay - Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs + Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs - An assay that uses a Giemsa stain to characterize cells. - Chris Stoeckert - Jie Zheng - https://github.com/obi-ontology/obi/issues/1093 - VEuPathDB + An assay that uses a Giemsa stain to characterize cells. + Chris Stoeckert + Jie Zheng + https://github.com/obi-ontology/obi/issues/1093 + VEuPathDB Giemsa stain assay @@ -71960,10 +77286,10 @@ https://www.doi.org/ individual organism specimen - A specimen composed of an individual organism to be studied in an investigation. - Person: Jie Zheng - EFO_0000542 individual - https://github.com/obi-ontology/obi/issues/1092 + A specimen composed of an individual organism to be studied in an investigation. + Person: Jie Zheng + EFO_0000542 individual + https://github.com/obi-ontology/obi/issues/1092 individual organism specimen @@ -72063,9 +77389,9 @@ https://www.doi.org/ blood microbiology assay - An organism identification assay that identifies a microorganism in a blood specimen. - John Judkins - https://github.com/obi-ontology/obi/issues/1064 + An organism identification assay that identifies a microorganism in a blood specimen. + John Judkins + https://github.com/obi-ontology/obi/issues/1064 blood microbiology assay @@ -72094,12 +77420,12 @@ https://www.doi.org/ biopsy - Biopsy of a potentially cancerous mole. + Biopsy of a potentially cancerous mole. - A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. - Damion Dooley - Nicole Vasilevsky - https://en.wikipedia.org/wiki/Biopsy + A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. + Damion Dooley + Nicole Vasilevsky + https://en.wikipedia.org/wiki/Biopsy biopsy @@ -72110,14 +77436,14 @@ https://www.doi.org/ image guided biopsy - Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. - - A biopsy which uses an imaging procedure to guide a needle biopsy. - Damion Dooley - image guided needle biopsy - image-guided biopsy - imaging guided biopsy - https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 + Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. + + A biopsy which uses an imaging procedure to guide a needle biopsy. + Damion Dooley + image guided needle biopsy + image-guided biopsy + imaging guided biopsy + https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 image guided biopsy @@ -72134,15 +77460,15 @@ https://www.doi.org/ computed tomography assisted biopsy - A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. - - A needle biopsy guided by real-time computed tomography (CT) scan images. - Damion Dooley - CT Assisted Biopsy - CT Guided Biopsy - Computed Tomography Assisted Biopsy - Computed Tomography-Guided Needle Biopsy - http://purl.obolibrary.org/obo/NCIT_C137909 + A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. + + A needle biopsy guided by real-time computed tomography (CT) scan images. + Damion Dooley + CT Assisted Biopsy + CT Guided Biopsy + Computed Tomography Assisted Biopsy + Computed Tomography-Guided Needle Biopsy + http://purl.obolibrary.org/obo/NCIT_C137909 computed tomography assisted biopsy @@ -72153,11 +77479,11 @@ https://www.doi.org/ ultrasound-guided needle biopsy - An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. + An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. - A needle biopsy guided by ultrasound visualization. - Damion Dooley - https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy + A needle biopsy guided by ultrasound visualization. + Damion Dooley + https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy ultrasound-guided needle biopsy @@ -72174,11 +77500,11 @@ https://www.doi.org/ needle biopsy - A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin. + A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin. - A biopsy that uses a hollow needle to extract cells. - Damion Dooley - https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 + A biopsy that uses a hollow needle to extract cells. + Damion Dooley + https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 needle biopsy @@ -72189,14 +77515,14 @@ https://www.doi.org/ fine needle aspiration biopsy - A fine needle aspiration biopsy is commonly performed in order to test for cancer. - - A biopsy that uses a thin needle to extract cells. - Chris Stoeckert, Helena Ellis, Jie Zheng - FNA - FNAB - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ - NCI BBRB + A fine needle aspiration biopsy is commonly performed in order to test for cancer. + + A biopsy that uses a thin needle to extract cells. + Chris Stoeckert, Helena Ellis, Jie Zheng + FNA + FNAB + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ + NCI BBRB fine needle aspiration biopsy @@ -72207,13 +77533,13 @@ https://www.doi.org/ core needle biopsy - A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed. + A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed. - A biopsy that uses a hollow tube to collect a core of tissue. - Chris Stoeckert, Helena Ellis, Jie Zheng - CNB - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ - NCI BBRB + A biopsy that uses a hollow tube to collect a core of tissue. + Chris Stoeckert, Helena Ellis, Jie Zheng + CNB + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ + NCI BBRB core needle biopsy @@ -72224,13 +77550,13 @@ https://www.doi.org/ surgical biopsy - Surgical biopsy may be required to collect hard-to-reach tissue. + Surgical biopsy may be required to collect hard-to-reach tissue. - A biopsy involving a surgical incision into an organism to access the biopsy material. - Damion Dooley - excisional biopsy - open biopsy - https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 + A biopsy involving a surgical incision into an organism to access the biopsy material. + Damion Dooley + excisional biopsy + open biopsy + https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 surgical biopsy @@ -72247,13 +77573,13 @@ https://www.doi.org/ abdominal wall fat pad biopsy - The makeup of fat in the abdominal wall can be investigated by fat biopsy. + The makeup of fat in the abdominal wall can be investigated by fat biopsy. - A biopsy involving the collection of a small part of the abdominal wall fat pad. - Nicole Vasilevsky, Damion Dooley - abdominal wall biopsy - fat biopsy - https://www.ucsfbenioffchildrens.org/tests/003841.html + A biopsy involving the collection of a small part of the abdominal wall fat pad. + Nicole Vasilevsky, Damion Dooley + abdominal wall biopsy + fat biopsy + https://www.ucsfbenioffchildrens.org/tests/003841.html abdominal wall fat pad biopsy @@ -72270,12 +77596,12 @@ https://www.doi.org/ tail biopsy - A mouse tail biopsy was performed to collect material for DNA extraction. + A mouse tail biopsy was performed to collect material for DNA extraction. - A biopsy involving the collection of the tip of a mamallian tail. - Nicole Vasilevsky, Damion Dooley - snip - http://web.jhu.edu/animalcare/policies/Tail%20Biopsy%20of%20Mice.pdf + A biopsy involving the collection of the tip of a mamallian tail. + Nicole Vasilevsky, Damion Dooley + snip + http://web.jhu.edu/animalcare/policies/Tail%20Biopsy%20of%20Mice.pdf tail biopsy @@ -72292,11 +77618,11 @@ https://www.doi.org/ bone marrow biopsy - A bone marrow biopsy removes bone with the marrow inside to look at under a microscope + A bone marrow biopsy removes bone with the marrow inside to look at under a microscope - A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. - Nicole Vasilevsky - http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy + A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. + Nicole Vasilevsky + http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy bone marrow biopsy @@ -72313,12 +77639,12 @@ https://www.doi.org/ skinpunch biopsy - A three or four millimeter punch is used in s skinpunch biopsy proceedure. + A three or four millimeter punch is used in s skinpunch biopsy proceedure. - A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool. - Nicole Vasilevsky - punch biopsy; skin biopsy - http://healthlibrary.epnet.com/GetContent.aspx?token=b93d114e-5009-4f6a-9917-6c594254fcc7&chunkiid=14861 + A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool. + Nicole Vasilevsky + punch biopsy; skin biopsy + http://healthlibrary.epnet.com/GetContent.aspx?token=b93d114e-5009-4f6a-9917-6c594254fcc7&chunkiid=14861 skinpunch biopsy @@ -72330,21 +77656,37 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-15 production by T cells - An assay of epitope specific interleukin-15 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-15 release|cytometric bead array + A cytometric bead array assay that detects interleukin-15 production by T cells. + IEDB + IEDB + IL-15 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-15 production by T cells @@ -72356,21 +77698,37 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-16 production by T cells - An assay of epitope specific interleukin-16 production by T cells that uses a cytometric bead array assay. - IEDB - IEDB - IL-16 release|cytometric bead array + A cytometric bead array assay that detects interleukin-16 production by T cells. + IEDB + IEDB + IL-16 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-16 production by T cells @@ -72394,10 +77752,10 @@ https://www.doi.org/ in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells - An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - hypersensitivity after adoptive transfer|in vivo assay + An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + hypersensitivity after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells @@ -72421,10 +77779,10 @@ https://www.doi.org/ in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells - An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test + An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells @@ -72457,10 +77815,10 @@ https://www.doi.org/ in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells - A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - proliferation after adoptive transfer|in vivo assay + A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + proliferation after adoptive transfer|in vivo assay in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells @@ -72484,10 +77842,10 @@ https://www.doi.org/ biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - antibody help after adoptive transfer|biological activity + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + antibody help after adoptive transfer|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells @@ -72511,10 +77869,10 @@ https://www.doi.org/ biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - T cell help after adoptive transfer|biological activity + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + T cell help after adoptive transfer|biological activity biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells @@ -72547,10 +77905,10 @@ https://www.doi.org/ in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells - A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - cytotoxicity after adoptive transfer|in vivo assay + A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + cytotoxicity after adoptive transfer|in vivo assay in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells @@ -72573,10 +77931,10 @@ https://www.doi.org/ ELISA measuring epitope specific perforin release by T cells - An assay of epitope specific perforin release by T cells that uses an ELISA. - IEDB - IEDB - perforin release|ELISA + An assay of epitope specific perforin release by T cells that uses an ELISA. + IEDB + IEDB + perforin release|ELISA ELISA measuring epitope specific perforin release by T cells @@ -72589,7 +77947,7 @@ https://www.doi.org/ enrichment culture medium Selenite broth is an enrichment culture medium used to selectively isolate Salmonella species. - A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest. + A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest. isolation medium @@ -72605,13 +77963,13 @@ https://www.doi.org/ - case series study design - PMID: 22213493 + case series study design + PMID: 22213493 - A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included. - http://orcid.org/0000-0002-8844-9165 - https://www.ncbi.nlm.nih.gov/pubmed/22213493 - case series design + A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included. + http://orcid.org/0000-0002-8844-9165 + https://www.ncbi.nlm.nih.gov/pubmed/22213493 + case series design @@ -72622,10 +77980,10 @@ https://www.doi.org/ massively parallel reporter assay - An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. - Damion Dooley - MPRA - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364389/ + An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. + Damion Dooley + MPRA + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364389/ massively parallel reporter assay @@ -72643,10 +78001,10 @@ https://www.doi.org/ in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells - An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - in vivo response after adoptive transfer|in vivo assay + An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + in vivo response after adoptive transfer|in vivo assay in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells @@ -72664,10 +78022,10 @@ https://www.doi.org/ in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells - An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - in vivo response after adoptive transfer|in vivo assay + An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + in vivo response after adoptive transfer|in vivo assay in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells @@ -72691,10 +78049,10 @@ https://www.doi.org/ in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells - An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - disease exacerbation after adoptive transfer|in vivo assay + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + disease exacerbation after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells @@ -72710,14 +78068,14 @@ https://www.doi.org/ - vacuum-assisted biopsy needle - Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source. + vacuum-assisted biopsy needle + Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source. - A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. - Damion Dooley - https://www.researchgate.net/publication/330227873 - https://github.com/obi-ontology/obi/issues/1163 - vacuum-assisted biopsy needle + A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. + Damion Dooley + https://www.researchgate.net/publication/330227873 + https://github.com/obi-ontology/obi/issues/1163 + vacuum-assisted biopsy needle @@ -72727,15 +78085,15 @@ https://www.doi.org/ pseudovirus entry assay - “Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387) - - An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. - Thomas Lemberger - pseudotype cell entry - pseudotype entry - pseudotyped particle cell entry assay - pseudovirus cell entry - Figure 1c in https://doi.org/10.1038/s41564-020-0688-y or Materials & Method in https://www.pnas.org/content/111/34/12516 + “Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387) + + An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. + Thomas Lemberger + pseudotype cell entry + pseudotype entry + pseudotyped particle cell entry assay + pseudovirus cell entry + Figure 1c in https://doi.org/10.1038/s41564-020-0688-y or Materials & Method in https://www.pnas.org/content/111/34/12516 pseudovirus entry assay @@ -72751,14 +78109,14 @@ https://www.doi.org/ - glass bottle + glass bottle - A container with a narrow neck that is made of glass. - VEuPathDB - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - glass bottle + A container with a narrow neck that is made of glass. + VEuPathDB + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + glass bottle @@ -72773,14 +78131,14 @@ https://www.doi.org/ - glass bottle coated with insecticides + glass bottle coated with insecticides - A glass bottle that coated with material designed to control insects. - VEuPathDB - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - glass bottle coated with insecticides + A glass bottle that coated with material designed to control insects. + VEuPathDB + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + glass bottle coated with insecticides @@ -72791,12 +78149,12 @@ https://www.doi.org/ short interspersed nuclear elements polymerase chain reaction - A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). - Jie Zheng - short interspersed elements PCR - PMID: 12711348 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). + Jie Zheng + short interspersed elements PCR + PMID: 12711348 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB short interspersed nuclear elements polymerase chain reaction @@ -72808,13 +78166,13 @@ https://www.doi.org/ nested polymerase chain reaction - A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction. - Jie Zheng - nested-PCR - nested PCR - https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction. + Jie Zheng + nested-PCR + nested PCR + https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB nested polymerase chain reaction @@ -72826,12 +78184,12 @@ https://www.doi.org/ immunoelectrophoresis - An electrophoresis that separates and characterize proteins based on reaction with antibodies. - Jie Zheng - IEP - https://en.wikipedia.org/wiki/Immunoelectrophoresis - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An electrophoresis that separates and characterize proteins based on reaction with antibodies. + Jie Zheng + IEP + https://en.wikipedia.org/wiki/Immunoelectrophoresis + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB immunoelectrophoresis @@ -72843,11 +78201,11 @@ https://www.doi.org/ counter current immunoelectrophoresis - An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions. - Jie Zheng - http://www.ispybio.com/search/protocols/ie%20protocol2.pdf - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions. + Jie Zheng + http://www.ispybio.com/search/protocols/ie%20protocol2.pdf + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB counter current immunoelectrophoresis @@ -72859,12 +78217,12 @@ https://www.doi.org/ ligase detection reaction - A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product. - Jie Zheng - LDR - MIRO:20000103 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product. + Jie Zheng + LDR + MIRO:20000103 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB ligase detection reaction @@ -72876,12 +78234,12 @@ https://www.doi.org/ loop-mediated isothermal amplification - An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR. - Jie Zheng - LAMP - https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR. + Jie Zheng + LAMP + https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB loop-mediated isothermal amplification @@ -72893,11 +78251,11 @@ https://www.doi.org/ detection of pathogenic organisms objective - An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB detection of pathogenic organisms objective @@ -72909,11 +78267,11 @@ https://www.doi.org/ insecticide resistance detection objective - An organism feature identification objective that aims to detect insecticide resistance of an insect. - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism feature identification objective that aims to detect insecticide resistance of an insect. + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance detection objective @@ -72924,16 +78282,16 @@ https://www.doi.org/ arthropod meal of blood specimen - A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. - - A specimen of the blood ingested by an arthropod. - The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. - Chris Stoeckert - Jie Zheng - blood meal - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. + + A specimen of the blood ingested by an arthropod. + The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. + Chris Stoeckert + Jie Zheng + blood meal + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB arthropod meal of blood specimen @@ -72956,11 +78314,11 @@ https://www.doi.org/ polymerase chain reaction assay - An assay that uses polymerase chain reaction technique to amplify DNA. - VEuPathDB - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An assay that uses polymerase chain reaction technique to amplify DNA. + VEuPathDB + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB polymerase chain reaction assay @@ -73060,14 +78418,14 @@ https://www.doi.org/ restriction fragment length polymorphism assay - An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. - VEuPathDB - RFLP - restriction fragment length polymorphism analysis - restriction fragment length polymorphism - https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. + VEuPathDB + RFLP + restriction fragment length polymorphism + restriction fragment length polymorphism analysis + https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB restriction fragment length polymorphism assay @@ -73113,15 +78471,15 @@ https://www.doi.org/ DNA fingerprinting assay - An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. - VEuPathDB - DNA finger printing - DNA fingerprint - DNA fingerprinting - DNA profiling - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. + VEuPathDB + DNA finger printing + DNA fingerprint + DNA fingerprinting + DNA profiling + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB DNA fingerprinting assay @@ -73144,12 +78502,12 @@ https://www.doi.org/ insecticide resistance assay - An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. - VEuPathDB - resistance identification/monitoring - MIRO:20000001 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. + VEuPathDB + resistance identification/monitoring + MIRO:20000001 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance assay @@ -73167,12 +78525,12 @@ https://www.doi.org/ insecticide resistance by monitoring known mutations assay - An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. - VEuPathDB - monitoring known mutations - MIRO:20000096 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. + VEuPathDB + monitoring known mutations + MIRO:20000096 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by monitoring known mutations assay @@ -73201,12 +78559,12 @@ https://www.doi.org/ insecticide resistance by detecting enzyme activity assay - An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. - VEuPathDB - metabolic resistance assay - MIRO:20000003 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. + VEuPathDB + metabolic resistance assay + MIRO:20000003 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting enzyme activity assay @@ -73224,12 +78582,12 @@ https://www.doi.org/ insecticide resistance bioassay - An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. - VEuPathDB - bioassay - MIRO:20000058 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. + VEuPathDB + bioassay + MIRO:20000058 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance bioassay @@ -73258,12 +78616,12 @@ https://www.doi.org/ insecticide resistance by detecting alpha esterase activity assay - An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. - VEuPathDB - alpha esterase activity assay - IRO:0000149 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. + VEuPathDB + alpha esterase activity assay + IRO:0000149 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting alpha esterase activity assay @@ -73292,12 +78650,12 @@ https://www.doi.org/ insecticide resistance by detecting beta esterase activity assay - An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. - VEuPathDB - beta esterase activity assay - IRO:0000150 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. + VEuPathDB + beta esterase activity assay + IRO:0000150 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting beta esterase activity assay @@ -73326,16 +78684,16 @@ https://www.doi.org/ insecticide resistance by detecting acetylcholinesterase activity assay - An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. - VEuPathDB - AChE activity assay - AChE assay - acetylcholinesterase assay - MIRO:20000010 - MIRO:20000084 - MIRO:20000086 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. + VEuPathDB + AChE activity assay + AChE assay + acetylcholinesterase assay + MIRO:20000010 + MIRO:20000084 + MIRO:20000086 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting acetylcholinesterase activity assay @@ -73364,12 +78722,12 @@ https://www.doi.org/ insecticide resistance by detecting glutathione S-transferase activity assay - An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). - VEuPathDB - GST related assay - MIRO:20000083 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). + VEuPathDB + GST related assay + MIRO:20000083 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting glutathione S-transferase activity assay @@ -73398,12 +78756,12 @@ https://www.doi.org/ insecticide resistance by detecting carboxylic ester hydrolase activity assay - An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. - VEuPathDB - pNPA assay - MIRO:20000019 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. + VEuPathDB + pNPA assay + MIRO:20000019 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting carboxylic ester hydrolase activity assay @@ -73421,12 +78779,12 @@ https://www.doi.org/ insecticide resistance by detecting mixed-function oxidase assay - An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. - VEuPathDB - mixed-function oxidase assay - MIRO:20000062 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. + VEuPathDB + mixed-function oxidase assay + MIRO:20000062 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by detecting mixed-function oxidase assay @@ -73444,12 +78802,12 @@ https://www.doi.org/ direct insecticide resistance bioassay - An insecticide resistance bioassay without the use of any synergist. - VEuPathDB - direct bioassay - MIRO:20000044 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance bioassay without the use of any synergist. + VEuPathDB + direct bioassay + MIRO:20000044 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB direct insecticide resistance bioassay @@ -73467,12 +78825,12 @@ https://www.doi.org/ topical application insecticide resistance bioassay - An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. - VEuPathDB - topical application assay - IRO:0000155 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. + VEuPathDB + topical application assay + IRO:0000155 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB topical application insecticide resistance bioassay @@ -73490,12 +78848,12 @@ https://www.doi.org/ direct insecticide resistance diagnostic assay - A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. - VEuPathDB - diagnostic test - MIRO:20000075 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. + VEuPathDB + diagnostic test + MIRO:20000075 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB direct insecticide resistance diagnostic assay @@ -73513,12 +78871,12 @@ https://www.doi.org/ insecticide resistance dose response assay - A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. - VEuPathDB - dose response test - MIRO:20000076 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. + VEuPathDB + dose response test + MIRO:20000076 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance dose response assay @@ -73536,12 +78894,12 @@ https://www.doi.org/ insecticide resistance time response assay - A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. - VEuPathDB - time response test - MIRO:20000013 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. + VEuPathDB + time response test + MIRO:20000013 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance time response assay @@ -73583,12 +78941,12 @@ https://www.doi.org/ Centre for Disease Control and Prevention bottle bioassay - A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. - VEuPathDB - CDC bottle bioassay - MIRO:20000009 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. + VEuPathDB + CDC bottle bioassay + MIRO:20000009 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB Centre for Disease Control and Prevention bottle bioassay @@ -73606,12 +78964,12 @@ https://www.doi.org/ WHO cone kit diagnostic assay - A direct insecticide resistance diagnostic assay uses WHO cone kit. - VEuPathDB - cone DT - MIRO:20000039 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance diagnostic assay uses WHO cone kit. + VEuPathDB + cone DT + MIRO:20000039 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB WHO cone kit diagnostic assay @@ -73629,12 +78987,12 @@ https://www.doi.org/ WHO paper kit diagnostic assay - A direct insecticide resistance diagnostic assay uses WHO paper kit. - VEuPathDB - WHO paper kit DT - MIRO:20000041 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance diagnostic assay uses WHO paper kit. + VEuPathDB + WHO paper kit DT + MIRO:20000041 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB WHO paper kit diagnostic assay @@ -73652,12 +79010,12 @@ https://www.doi.org/ WHO larvicide diagnostic assay - A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. - VEuPathDB - WHO larvicide DT - MIRO:20000049 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. + VEuPathDB + WHO larvicide DT + MIRO:20000049 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB WHO larvicide diagnostic assay @@ -73699,12 +79057,12 @@ https://www.doi.org/ insecticide resistance dose response by bottle assay - An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. - VEuPathDB - bottle bioassay DR test - MIRO:20000011 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. + VEuPathDB + bottle bioassay DR test + MIRO:20000011 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance dose response by bottle assay @@ -73722,12 +79080,12 @@ https://www.doi.org/ insecticide resistance dose response by survival of larvae assay - An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. - VEuPathDB - WHO larvicide DR test - MIRO:20000050 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. + VEuPathDB + WHO larvicide DR test + MIRO:20000050 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance dose response by survival of larvae assay @@ -73745,12 +79103,12 @@ https://www.doi.org/ insecticide resistance dose response by WHO paper kit assay - An insecticide resistance dose response assay using WHO paper kit. - VEuPathDB - WHO paper kit DR test - MIRO:20000048 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance dose response assay using WHO paper kit. + VEuPathDB + WHO paper kit DR test + MIRO:20000048 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance dose response by WHO paper kit assay @@ -73792,12 +79150,12 @@ https://www.doi.org/ insecticide resistance time response by bottle assay - An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. - VEuPathDB - bottle bioassay TR test - MIRO:20000030 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. + VEuPathDB + bottle bioassay TR test + MIRO:20000030 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance time response by bottle assay @@ -73815,12 +79173,12 @@ https://www.doi.org/ insecticide resistance time response by WHO paper kit assay - An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. - VEuPathDB - WHO paper kit TR test - MIRO:20000036 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. + VEuPathDB + WHO paper kit TR test + MIRO:20000036 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance time response by WHO paper kit assay @@ -73879,14 +79237,14 @@ https://www.doi.org/ insecticide resistance by amplification refractory mutation system assay - An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. - VEuPathDB - ARMS - Amplification Refractory Mutation System - IRO:0000006 - PMID: 18428319 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. + VEuPathDB + ARMS + Amplification Refractory Mutation System + IRO:0000006 + PMID: 18428319 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by amplification refractory mutation system assay @@ -73951,15 +79309,15 @@ https://www.doi.org/ insecticide resistance by primer introduced restriction analysis PCR assay - An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. - VEuPathDB - PIRA-PCR - polymerase chain reaction-primer-introduced restriction analysis - Primer Introduced Restriction Analysis PCR - IRO:0000007 - PMID: 8339229 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. + VEuPathDB + PIRA-PCR + Primer Introduced Restriction Analysis PCR + polymerase chain reaction-primer-introduced restriction analysis + IRO:0000007 + PMID: 8339229 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by primer introduced restriction analysis PCR assay @@ -74018,12 +79376,12 @@ https://www.doi.org/ insecticide resistance by nested polymerase chain reaction assay - An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. - VEuPathDB - gene mutation detection by nested PCR - IRO:0000127 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. + VEuPathDB + gene mutation detection by nested PCR + IRO:0000127 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by nested polymerase chain reaction assay @@ -74081,11 +79439,11 @@ https://www.doi.org/ insecticide resistance by ligase detection reaction assay - An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. - VEuPathDB - MIRO:20000103 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. + VEuPathDB + MIRO:20000103 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by ligase detection reaction assay @@ -74143,13 +79501,13 @@ https://www.doi.org/ insecticide resistance by ligase detection reaction-fluorescent microsphere assay - An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. - VEuPathDB - ligase detection reaction-fluorescent microsphere assay - gene mutation detection by LDR-FMA - IRO:0000151 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. + VEuPathDB + gene mutation detection by LDR-FMA + ligase detection reaction-fluorescent microsphere assay + IRO:0000151 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by ligase detection reaction-fluorescent microsphere assay @@ -74208,14 +79566,14 @@ https://www.doi.org/ insecticide resistance by PCR amplification of specific alleles assay - An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. - VEuPathDB - PCR amplification of specific alleles - allele-specific amplification and amplification refractory mutation system - PASA - PMID: 1734929 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. + VEuPathDB + PASA + PCR amplification of specific alleles + allele-specific amplification and amplification refractory mutation system + PMID: 1734929 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by PCR amplification of specific alleles assay @@ -74274,11 +79632,11 @@ https://www.doi.org/ insecticide resistance by fluorogenic PCR assay - An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. - VEuPathDB - MIRO:20000102 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. + VEuPathDB + MIRO:20000102 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by fluorogenic PCR assay @@ -74343,12 +79701,12 @@ https://www.doi.org/ insecticide resistance by PCR-RELP assay - An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. - VEuPathDB - PCR-RFLP - MIRO:20000113 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. + VEuPathDB + PCR-RFLP + MIRO:20000113 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by PCR-RELP assay @@ -74407,12 +79765,12 @@ https://www.doi.org/ insecticide resistance by short interspersed elements PCR assay - An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). - VEuPathDB - Short Interspersed Elements PCR - IRO:0000013 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). + VEuPathDB + Short Interspersed Elements PCR + IRO:0000013 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB insecticide resistance by short interspersed elements PCR assay @@ -74444,12 +79802,12 @@ https://www.doi.org/ pathogen detection assay - An organism identification assay that aims to detect pathogens. - VEuPathDB - pathogen detection method - IRO:0000137 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that aims to detect pathogens. + VEuPathDB + pathogen detection method + IRO:0000137 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB pathogen detection assay @@ -74478,12 +79836,12 @@ https://www.doi.org/ VectorTest assay - A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. - VEuPathDB - VectorTest - IRO:0000138 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. + VEuPathDB + VectorTest + IRO:0000138 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB VectorTest assay @@ -74512,12 +79870,12 @@ https://www.doi.org/ pathogen detection by Rapid Analyte Measurement Platform assay - A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. - VEuPathDB - Rapid Analyte Measurement Platform - IRO:0000164 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. + VEuPathDB + Rapid Analyte Measurement Platform + IRO:0000164 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB pathogen detection by Rapid Analyte Measurement Platform assay @@ -74552,12 +79910,12 @@ https://www.doi.org/ pathogen detection by loop-mediated isothermal amplification assay - A pathogen detection assay that is based on loop-mediated isothermal amplification. - VEuPathDB - Loop-mediated isothermal amplification - IRO:0000165 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A pathogen detection assay that is based on loop-mediated isothermal amplification. + VEuPathDB + Loop-mediated isothermal amplification + IRO:0000165 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB pathogen detection by loop-mediated isothermal amplification assay @@ -74580,12 +79938,12 @@ https://www.doi.org/ blood meal assay - An assay that analyzes the specimen taken from blood meal fed organism, such as insect. - VEuPathDB - blood meal analysis - IRO:0000135 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An assay that analyzes the specimen taken from blood meal fed organism, such as insect. + VEuPathDB + blood meal analysis + IRO:0000135 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB blood meal assay @@ -74609,13 +79967,13 @@ https://www.doi.org/ blood meal by counter current immunoelectrophoresis assay - A blood meal assay that uses a counter current immunoelectrophoresis technique. - VEuPathDB - CIE - countercurrent immunoelectrophoresis - IRO:0000136 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A blood meal assay that uses a counter current immunoelectrophoresis technique. + VEuPathDB + CIE + countercurrent immunoelectrophoresis + IRO:0000136 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB blood meal by counter current immunoelectrophoresis assay @@ -74668,13 +80026,13 @@ https://www.doi.org/ DNA based blood meal finger printing assay - A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. - VEuPathDB - DNA based blood meal finger printing - VSMO:0001307 - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. + VEuPathDB + DNA based blood meal finger printing + VEuPathDB + VSMO:0001307 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB DNA based blood meal finger printing assay @@ -74692,12 +80050,12 @@ https://www.doi.org/ organism identification by size assay - An organism identification assay that is based on the size of organism. - VEuPathDB - by size - IRO:0000145 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on the size of organism. + VEuPathDB + by size + IRO:0000145 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by size assay @@ -74715,12 +80073,12 @@ https://www.doi.org/ organism identification by cross mating assay - An organism identification assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. - VEuPathDB - cross mating experiment - MIRO:30000036 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. + VEuPathDB + cross mating experiment + MIRO:30000036 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by cross mating assay @@ -74738,12 +80096,12 @@ https://www.doi.org/ organism identification by cytological chromosome examination assay - An organism identification assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. - VEuPathDB - cytological chromosome examination - MIRO:30000037 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. + VEuPathDB + cytological chromosome examination + MIRO:30000037 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by cytological chromosome examination assay @@ -74767,12 +80125,12 @@ https://www.doi.org/ organism identification by isoenzyme electrophoresis assay - An organism identification assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. - VEuPathDB - isoenzyme electrophoresis - MIRO:30000038 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. + VEuPathDB + isoenzyme electrophoresis + MIRO:30000038 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by isoenzyme electrophoresis assay @@ -74790,12 +80148,12 @@ https://www.doi.org/ organism identification by morphological examination assay - An organism identification assay that is based on examination of morphology and the use of specific "taxonomic keys" to determine the species of the specimen. - VEuPathDB - morphological examination - MIRO:30000039 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on examination of morphology and the use of specific "taxonomic keys" to determine the species of the specimen. + VEuPathDB + morphological examination + MIRO:30000039 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by morphological examination assay @@ -74820,12 +80178,12 @@ https://www.doi.org/ organism identification by PCR assay - An organism identification assay that is based on PCR. - VEuPathDB - PCR-based species identification - MIRO:30000040 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on PCR. + VEuPathDB + PCR-based species identification + MIRO:30000040 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by PCR assay @@ -74849,12 +80207,12 @@ https://www.doi.org/ organism identification by specific DNA hybridization assay - An organism identification assay that is based on DNA hybrdization. - VEuPathDB - species specific DNA hybridization - MIRO:30000041 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay that is based on DNA hybrdization. + VEuPathDB + species specific DNA hybridization + MIRO:30000041 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by specific DNA hybridization assay @@ -74872,12 +80230,12 @@ https://www.doi.org/ organism identification by salinity tolerance assay - An organism identification assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. - VEuPathDB - salinity tolerance tests - MIRO:30000042 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB + An organism identification assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. + VEuPathDB + salinity tolerance tests + MIRO:30000042 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB organism identification by salinity tolerance assay @@ -74941,12 +80299,12 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist vacuum-assisted biopsy - A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue. + A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue. - A biopsy performed with a needle augmented with a vacuum device. - Damion Dooley - VAB - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ + A biopsy performed with a needle augmented with a vacuum device. + Damion Dooley + VAB + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ vacuum-assisted biopsy @@ -74973,9 +80331,9 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist induced sputum specimen - A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. - John Judkins - PMC3297553 + A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. + John Judkins + PMC3297553 induced sputum specimen @@ -75027,14 +80385,14 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - Oxford Nanopore MinION - Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION + Oxford Nanopore MinION + Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION - A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - PERSON: Bonita Lam - ONT MinION, MinION - https://nanoporetech.com/products/minion - Oxford Nanopore MinION + A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + PERSON: Bonita Lam + ONT MinION, MinION + https://nanoporetech.com/products/minion + Oxford Nanopore MinION @@ -75049,14 +80407,14 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - Oxford Nanopore GridION Mk1 - Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer + Oxford Nanopore GridION Mk1 + Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. - PERSON: Bonita Lam - Oxford Nanopore GridION X5, GridION Mk1 - https://nanoporetech.com/products/gridion - Oxford Nanopore GridION Mk1 + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. + PERSON: Bonita Lam + Oxford Nanopore GridION X5, GridION Mk1 + https://nanoporetech.com/products/gridion + Oxford Nanopore GridION Mk1 @@ -75071,14 +80429,14 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - Oxford Nanopore PromethION - Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. + Oxford Nanopore PromethION + Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - PERSON: Bonita Lam - PromethION - https://nanoporetech.com/products/promethion - Oxford Nanopore PromethION + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + PERSON: Bonita Lam + PromethION + https://nanoporetech.com/products/promethion + Oxford Nanopore PromethION @@ -75086,7 +80444,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -75096,10 +80454,10 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist PRO-cap - Precision nuclear run-on and sequencing to detect Pol II initiation sites - Bonita Lam - PRO-CAP - https://github.com/obi-ontology/obi/issues/1102 + Precision nuclear run-on and sequencing to detect Pol II initiation sites + Bonita Lam + PRO-CAP + https://github.com/obi-ontology/obi/issues/1102 PRO-cap @@ -75157,13 +80515,13 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s ribosomal RNA-depleted RNA sequencing assay - An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - rRNA-deleted RNA sequencing assay - PMID:29556074 - CFDE + An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + rRNA-deleted RNA sequencing assay + PMID:29556074 + CFDE ribosomal RNA-depleted RNA sequencing assay @@ -75181,12 +80539,12 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s metatranscriptome sequencing assay - An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:31450270 - CFDE + An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:31450270 + CFDE metatranscriptome sequencing assay @@ -75198,13 +80556,13 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s lipid profiling assay - An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - lipidomic assay - OBI metabolite profiling assay - CFDE + An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + lipidomic assay + OBI metabolite profiling assay + CFDE lipid profiling assay @@ -75215,14 +80573,14 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s single-nucleus ATAC-seq - snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge. - - An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - snATAC-seq - http://www.biorxiv.org/content/early/2017/07/06/159137 - https://github.com/obi-ontology/obi/issues/864 - ENCODE + snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge. + + An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + snATAC-seq + http://www.biorxiv.org/content/early/2017/07/06/159137 + https://github.com/obi-ontology/obi/issues/864 + ENCODE single-nucleus ATAC-seq @@ -75252,13 +80610,13 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s 16s ribosomal gene sequencing assay - An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - 16S rRNA sequencing assay - PMID:31450270 - CFDE + An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + 16S rRNA sequencing assay + PMID:31450270 + CFDE 16s ribosomal gene sequencing assay @@ -75270,12 +80628,12 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s single-cell ATAC-seq - An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - scATAC-seq - http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html - https://github.com/obi-ontology/obi/issues/864 - ENCODE + An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + scATAC-seq + http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html + https://github.com/obi-ontology/obi/issues/864 + ENCODE single-cell ATAC-seq @@ -75339,13 +80697,13 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s microbiome protein expression profiling assay - A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - metaproteomic assay - PMID:31450270 - CFDE + A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + metaproteomic assay + PMID:31450270 + CFDE microbiome protein expression profiling assay @@ -75357,12 +80715,12 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s cytokine assay - An analyte assay to study presence, concentration, or amount of cytokines. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:23603216 - CFDE + An analyte assay to study presence, concentration, or amount of cytokines. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:23603216 + CFDE cytokine assay @@ -75432,13 +80790,13 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s amplicon sequencing assay - A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:29628929 - PMID:31450270 - CFDE + A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:29628929 + PMID:31450270 + CFDE amplicon sequencing assay @@ -75450,12 +80808,12 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s whole virome sequencing assay - A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - OBI:0002623 - CFDE + A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + OBI:0002623 + CFDE whole virome sequencing assay @@ -75537,15 +80895,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre single-value binding of antibody with reporter to antigen assay - Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2. - - An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest - LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA) - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - IA - immunoassay - LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47 - https://github.com/obi-ontology/obi/issues/1203 + Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2. + + An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest + LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA) + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + IA + immunoassay + LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47 + https://github.com/obi-ontology/obi/issues/1203 single-value binding of antibody with reporter to antigen assay @@ -75577,6 +80935,36 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + cytometry analysis by automated gating + + A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest. + Bjoern Peters + CMI-PB + https://github.com/obi-ontology/obi/issues/1226 + cytometry analysis by automated gating + + + + + + + + + cytometry analysis by manual gating + + A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest. + Bjoern Peters + CMI-PB + https://github.com/obi-ontology/obi/issues/1226 + cytometry analysis by manual gating + + + + @@ -75604,10 +80992,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre tracheal aspirate specimen - A specimen that is collected with a suctioning tube from the trachea. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - tracheal wash specimen - PMID:25338241 + A specimen that is collected with a suctioning tube from the trachea. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + tracheal wash specimen + PMID:25338241 tracheal aspirate specimen @@ -75644,9 +81032,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre mid-turbinate nasal swab specimen - A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 + A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 mid-turbinate nasal swab specimen @@ -75683,10 +81071,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre nasal aspirate specimen - A specimen that is collected with a suctioning tube from the nasal cavity. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - nasal wash specimen|nasopharyngeal aspirate - Asiyah Yu Lin ORCID:0000-0003-2620-0345 + A specimen that is collected with a suctioning tube from the nasal cavity. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + nasal wash specimen|nasopharyngeal aspirate + Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen @@ -75723,10 +81111,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre lower respiratory tract aspirate specimen - A specimen that is collected with a suctioning tube from the lower respiratory tract. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - lower respiratory tract wash specimen - Asiyah Yu Lin ORCID:0000-0003-2620-0345 + A specimen that is collected with a suctioning tube from the lower respiratory tract. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + lower respiratory tract wash specimen + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract aspirate specimen @@ -75763,9 +81151,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre upper respiratory specimen - A specimen that is derived from the upper respiratory tract - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 + A specimen that is derived from the upper respiratory tract + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 upper respiratory specimen @@ -75802,9 +81190,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre lower respiratory tract specimen - A specimen that is derived from the lower respiratory tract. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 + A specimen that is derived from the lower respiratory tract. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract specimen @@ -75841,9 +81229,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre anterior nasal swab specimen - A specimen that is derived from the anterior nasal wall - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 + A specimen that is derived from the anterior nasal wall + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 anterior nasal swab specimen @@ -75855,9 +81243,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre aspiration specimen collection - Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 - aspiration procedure + Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. + Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + aspiration procedure https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631 aspiration specimen collection @@ -75868,17 +81256,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - personal protective device - Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. - PPE is equipment worn by a worker to minimize exposure to specific hazards. + personal protective device + Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. + PPE is equipment worn by a worker to minimize exposure to specific hazards. - A device which is a wearable garment designed to protect the wearer's body from injury or infection. - https://orcid.org/0000-0002-8844-9165 - PPE - personal protective equipment - https://en.wikipedia.org/wiki/Personal_protective_equipment - https://github.com/obi-ontology/obi/issues/1193 - personal protective device + A device which is a wearable garment designed to protect the wearer's body from injury or infection. + https://orcid.org/0000-0002-8844-9165 + PPE + personal protective equipment + https://en.wikipedia.org/wiki/Personal_protective_equipment + https://github.com/obi-ontology/obi/issues/1193 + personal protective device @@ -75887,16 +81275,16 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - face mask - A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings + face mask + A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings - A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles. - https://orcid.org/0000-0002-8844-9165 - face covering - respirator - Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask - https://github.com/obi-ontology/obi/issues/1193 - face mask + A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles. + https://orcid.org/0000-0002-8844-9165 + face covering + respirator + Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask + https://github.com/obi-ontology/obi/issues/1193 + face mask @@ -75905,15 +81293,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - non-medical mask - A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth. + non-medical mask + A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth. - A face mask not manufactured according to medical equipment standards. - https://orcid.org/0000-0002-8844-9165 - cloth mask - https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html - https://github.com/obi-ontology/obi/issues/1193 - non-medical mask + A face mask not manufactured according to medical equipment standards. + https://orcid.org/0000-0002-8844-9165 + cloth mask + https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html + https://github.com/obi-ontology/obi/issues/1193 + non-medical mask @@ -75922,15 +81310,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - medical mask - The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both. + medical mask + The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both. - A face mask manufactured according to a recognized medical equipment standard. - https://orcid.org/0000-0002-9578-0788 - surgical mask - https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html - https://github.com/obi-ontology/obi/issues/1193 - medical mask + A face mask manufactured according to a recognized medical equipment standard. + https://orcid.org/0000-0002-9578-0788 + surgical mask + https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html + https://github.com/obi-ontology/obi/issues/1193 + medical mask @@ -75939,17 +81327,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - N95 respirator + N95 respirator - A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles. - https://orcid.org/0000-0002-8844-9165 - N95 - N95 face mask - N95 facemask - N95 respirator mask - https://en.wikipedia.org/wiki/N95_mask - https://github.com/obi-ontology/obi/issues/1193 - N95 respirator + A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles. + https://orcid.org/0000-0002-8844-9165 + N95 + N95 face mask + N95 facemask + N95 respirator mask + https://en.wikipedia.org/wiki/N95_mask + https://github.com/obi-ontology/obi/issues/1193 + N95 respirator @@ -75958,15 +81346,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - face shield + face shield - A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials. - https://orcid.org/0000-0002-8844-9165 - faceshield - splash shield - https://en.wikipedia.org/wiki/Face_shield - https://github.com/obi-ontology/obi/issues/1193 - face shield + A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials. + https://orcid.org/0000-0002-8844-9165 + faceshield + splash shield + https://en.wikipedia.org/wiki/Face_shield + https://github.com/obi-ontology/obi/issues/1193 + face shield @@ -75975,14 +81363,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - patient gown + patient gown - A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. - https://orcid.org/0000-0002-8844-9165 - hospital gown - https://en.wikipedia.org/wiki/Patient_gown - https://github.com/obi-ontology/obi/issues/1193 - patient gown + A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. + https://orcid.org/0000-0002-8844-9165 + hospital gown + https://en.wikipedia.org/wiki/Patient_gown + https://github.com/obi-ontology/obi/issues/1193 + patient gown @@ -75991,15 +81379,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - scrubs - Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes. + scrubs + Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes. - A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap. - https://orcid.org/0000-0002-8844-9165 - scrub clothing item - https://en.wikipedia.org/wiki/Scrubs_(clothing) - https://github.com/obi-ontology/obi/issues/1193 - scrubs + A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap. + https://orcid.org/0000-0002-8844-9165 + scrub clothing item + https://en.wikipedia.org/wiki/Scrubs_(clothing) + https://github.com/obi-ontology/obi/issues/1193 + scrubs @@ -76008,13 +81396,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - reusable patient gown + reusable patient gown - A patient gown intended to be reused after being laundered. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Patient_gown - https://github.com/obi-ontology/obi/issues/1193 - reusable patient gown + A patient gown intended to be reused after being laundered. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Patient_gown + https://github.com/obi-ontology/obi/issues/1193 + reusable patient gown @@ -76023,13 +81411,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - disposable patient gown + disposable patient gown - A patient gown intended for a single period of continuous use and then disposed of. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Patient_gown - https://github.com/obi-ontology/obi/issues/1193 - disposable patient gown + A patient gown intended for a single period of continuous use and then disposed of. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Patient_gown + https://github.com/obi-ontology/obi/issues/1193 + disposable patient gown @@ -76038,14 +81426,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - medical gown + medical gown - A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional. - https://orcid.org/0000-0002-8844-9165 - hospital gown - https://en.wikipedia.org/wiki/Medical_gown - https://github.com/obi-ontology/obi/issues/1193 - medical gown + A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional. + https://orcid.org/0000-0002-8844-9165 + hospital gown + https://en.wikipedia.org/wiki/Medical_gown + https://github.com/obi-ontology/obi/issues/1193 + medical gown @@ -76054,13 +81442,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - apron + apron - A garment which is worn over other clothing and covers mainly the front of the body. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Apron - https://github.com/obi-ontology/obi/issues/1193 - apron + A garment which is worn over other clothing and covers mainly the front of the body. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Apron + https://github.com/obi-ontology/obi/issues/1193 + apron @@ -76069,13 +81457,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - surgical gown + surgical gown - A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - surgical gown + A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + surgical gown @@ -76084,13 +81472,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - personal protective glove + personal protective glove - A personal protective device which is a glove. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - personal protective glove + A personal protective device which is a glove. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + personal protective glove @@ -76099,13 +81487,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - personal protective clothing item + personal protective clothing item - A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - personal protective clothing item + A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + personal protective clothing item @@ -76114,14 +81502,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - laboratory coat + laboratory coat - A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. - https://orcid.org/0000-0002-8844-9165 - white coat - https://en.wikipedia.org/wiki/White_coat - https://github.com/obi-ontology/obi/issues/1193 - laboratory coat + A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. + https://orcid.org/0000-0002-8844-9165 + white coat + https://en.wikipedia.org/wiki/White_coat + https://github.com/obi-ontology/obi/issues/1193 + laboratory coat @@ -76130,13 +81518,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - medical glove + medical glove - A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Medical_glove - https://github.com/obi-ontology/obi/issues/1193 - medical glove + A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Medical_glove + https://github.com/obi-ontology/obi/issues/1193 + medical glove @@ -76145,13 +81533,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - nitrile glove + nitrile glove - A personal protective glove which is made out of nitrile rubber. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Medical_glove - https://github.com/obi-ontology/obi/issues/1193 - nitrile glove + A personal protective glove which is made out of nitrile rubber. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Medical_glove + https://github.com/obi-ontology/obi/issues/1193 + nitrile glove @@ -76160,14 +81548,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - transparent partition + transparent partition - A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. - https://orcid.org/0000-0002-8844-9165 - transparent partition - https://ncceh.ca/content/blog/physical-barriers-covid-19-infection-prevention-and-control-commercial-settings - https://github.com/obi-ontology/obi/issues/1193 - transparent droplet barrier + A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. + https://orcid.org/0000-0002-8844-9165 + transparent partition + https://ncceh.ca/content/blog/physical-barriers-covid-19-infection-prevention-and-control-commercial-settings + https://github.com/obi-ontology/obi/issues/1193 + transparent droplet barrier @@ -76176,15 +81564,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - footwear cover + footwear cover - A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. - https://orcid.org/0000-0002-8844-9165 - boot cover - shoe cover - https://en.wiktionary.org/wiki/shoecover - https://github.com/obi-ontology/obi/issues/1193 - footwear cover + A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. + https://orcid.org/0000-0002-8844-9165 + boot cover + shoe cover + https://en.wiktionary.org/wiki/shoecover + https://github.com/obi-ontology/obi/issues/1193 + footwear cover @@ -76193,13 +81581,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - disposable footwear cover + disposable footwear cover - A footwear cover which is designed for a single period of continuous use and then disposed of. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - disposable footwear cover + A footwear cover which is designed for a single period of continuous use and then disposed of. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + disposable footwear cover @@ -76208,13 +81596,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - reusable footwear cover + reusable footwear cover - A footwear cover which is designed for repeated use. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - reusable footwear cover + A footwear cover which is designed for repeated use. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + reusable footwear cover @@ -76223,17 +81611,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - surgical N95 respirator + surgical N95 respirator - A N95 respirator which has been approved by the FDA as a surgical mask. - https://orcid.org/0000-0002-8844-9165 - healthcare respirator - medical respirator - surgical N95 - surgical N95 respirator - https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf - https://github.com/obi-ontology/obi/issues/1193 - surgical N95 respirator + A N95 respirator which has been approved by the FDA as a surgical mask. + https://orcid.org/0000-0002-8844-9165 + healthcare respirator + medical respirator + surgical N95 + surgical N95 respirator + https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf + https://github.com/obi-ontology/obi/issues/1193 + surgical N95 respirator @@ -76242,13 +81630,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - protective coverall + protective coverall - A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination. - https://orcid.org/0000-0002-8844-9165 - https://www.safeopedia.com/definition/863/disposable-coveralls - https://github.com/obi-ontology/obi/issues/1193 - protective coverall + A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination. + https://orcid.org/0000-0002-8844-9165 + https://www.safeopedia.com/definition/863/disposable-coveralls + https://github.com/obi-ontology/obi/issues/1193 + protective coverall @@ -76257,14 +81645,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - protective sleeve - A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids. + protective sleeve + A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids. - A personal protective clothing item which is a protective cover worn over the arm. - https://orcid.org/0000-0002-8844-9165 - https://www.safeopedia.com/definition/974/protective-sleeves - https://github.com/obi-ontology/obi/issues/1193 - protective sleeve + A personal protective clothing item which is a protective cover worn over the arm. + https://orcid.org/0000-0002-8844-9165 + https://www.safeopedia.com/definition/974/protective-sleeves + https://github.com/obi-ontology/obi/issues/1193 + protective sleeve @@ -76273,13 +81661,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - protective apron + protective apron - A personal protective clothing item which is an apron. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Apron - https://github.com/obi-ontology/obi/issues/1193 - protective apron + A personal protective clothing item which is an apron. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Apron + https://github.com/obi-ontology/obi/issues/1193 + protective apron @@ -76288,18 +81676,18 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - medical cap + medical cap - A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. - https://orcid.org/0000-0002-8844-9165 - bouffant cap - bouffant hat - medical bonnet - scrub cap - surgical hat - https://en.wikipedia.org/wiki/Scrubs_(clothing) - https://github.com/obi-ontology/obi/issues/1193 - medical cap + A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. + https://orcid.org/0000-0002-8844-9165 + bouffant cap + bouffant hat + medical bonnet + scrub cap + surgical hat + https://en.wikipedia.org/wiki/Scrubs_(clothing) + https://github.com/obi-ontology/obi/issues/1193 + medical cap @@ -76308,11 +81696,26 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - specimen collection device + specimen collection device - A container used to collect a specimen. - https://orcid.org/0000-0002-8844-9165 - specimen collection device + A container used to collect a specimen. + https://orcid.org/0000-0002-8844-9165 + specimen collection device + + + + + + + + + chromatography vial + + A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 + chromatography vial @@ -76321,20 +81724,20 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - specimen pad - An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples. + specimen pad + An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples. - A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. - https://orcid.org/0000-0002-8844-9165 - absorbant pad - polysponge - sample pad - sampling sponge - specimen sponge - surface wipe - swab - Derived from NCIT sponge definition. - specimen pad + A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. + https://orcid.org/0000-0002-8844-9165 + absorbant pad + polysponge + sample pad + sampling sponge + specimen sponge + surface wipe + swab + Derived from NCIT sponge definition. + specimen pad @@ -76343,17 +81746,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - specimen collection swab stick - A swab stick allows a worker to collect samples without touching the inside of the bag + specimen collection swab stick + A swab stick allows a worker to collect samples without touching the inside of the bag - A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material. - https://orcid.org/0000-0002-8844-9165 - sponge stick - polyprobe - sponge probe - sponge-stick - https://medical-dictionary.thefreedictionary.com/swab - specimen collection swab stick + A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material. + https://orcid.org/0000-0002-8844-9165 + polyprobe + sponge probe + sponge stick + sponge-stick + https://medical-dictionary.thefreedictionary.com/swab + specimen collection swab stick @@ -76362,14 +81765,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - cotton swab + cotton swab - A device which is a cotton pad mounted on one or both ends of a stick. - https://orcid.org/0000-0002-8844-9165 - Q-tip - swab-sampler - https://en.wikipedia.org/wiki/Cotton_swab - cotton swab + A device which is a cotton pad mounted on one or both ends of a stick. + https://orcid.org/0000-0002-8844-9165 + Q-tip + swab-sampler + https://en.wikipedia.org/wiki/Cotton_swab + cotton swab @@ -76384,12 +81787,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - drag swab + drag swab - A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string - https://orcid.org/0000-0002-8844-9165 - https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses - drag swab + A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string + https://orcid.org/0000-0002-8844-9165 + https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses + drag swab @@ -76398,11 +81801,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - pre-moistened swab stick + pre-moistened swab stick - A specimen collection swab stick that is pre-moistened with liquid prior to sampling. - https://orcid.org/0000-0002-8844-9165 - pre-moistened swab stick + A specimen collection swab stick that is pre-moistened with liquid prior to sampling. + https://orcid.org/0000-0002-8844-9165 + pre-moistened swab stick @@ -76411,13 +81814,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - surface wipe - Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air. + surface wipe + Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air. - A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. - https://orcid.org/0000-0002-8844-9165 - https://www.science.gov/topicpages/s/surface+wipe+sampling.html - surface wipe + A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. + https://orcid.org/0000-0002-8844-9165 + https://www.science.gov/topicpages/s/surface+wipe+sampling.html + surface wipe @@ -76474,15 +81877,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - ultraviolet light source + ultraviolet light source - A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. - Person: Jie Zheng - UV light source - Person: Jie Zheng - https://github.com/obi-ontology/obi/issues/1200 - VEuPathDB - ultraviolet light source + A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. + Person: Jie Zheng + UV light source + Person: Jie Zheng + https://github.com/obi-ontology/obi/issues/1200 + VEuPathDB + ultraviolet light source @@ -76491,14 +81894,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - visible light source + visible light source - A light source that provides visible light for use in a distant area using a delivery system. - Person: Jie Zheng - Person: Jie Zheng - https://github.com/obi-ontology/obi/issues/1200 - VEuPathDB - visible light source + A light source that provides visible light for use in a distant area using a delivery system. + Person: Jie Zheng + Person: Jie Zheng + https://github.com/obi-ontology/obi/issues/1200 + VEuPathDB + visible light source @@ -76507,16 +81910,16 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - solar light source + solar light source - A light source that light is produced from solar energy. - Person: Chris Stoeckert - Person: Jie Zheng - Person: Chris Stoeckert - Person: Jie Zheng - https://github.com/obi-ontology/obi/issues/1200 - VEuPathDB - solar light source + A light source that light is produced from solar energy. + Person: Chris Stoeckert + Person: Jie Zheng + Person: Chris Stoeckert + Person: Jie Zheng + https://github.com/obi-ontology/obi/issues/1200 + VEuPathDB + solar light source @@ -76527,11 +81930,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre adult arthropod specimen collection process - A live arthropod specimen collection process in which the arthropods are in the adult stage. - John Judkins - collection of adults - MIRO:30000052 - https://github.com/obi-ontology/obi/issues/1217 + A live arthropod specimen collection process in which the arthropods are in the adult stage. + John Judkins + collection of adults + MIRO:30000052 + https://github.com/obi-ontology/obi/issues/1217 adult arthropod specimen collection process @@ -76543,11 +81946,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre animal-biting arthropod specimen collection by aspiration - An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. - John Judkins - animal biting catch - MIRO:30000012 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. + John Judkins + animal biting catch + MIRO:30000012 + https://github.com/obi-ontology/obi/issues/1217 animal-biting arthropod specimen collection by aspiration @@ -76559,11 +81962,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre animal-biting outdoor arthropod specimen collection by aspiration - An animal-biting arthropod specimen collection by aspiration that occurs outside a building. - John Judkins - animal biting catch - outdoors - MIRO:30000014 - https://github.com/obi-ontology/obi/issues/1217 + An animal-biting arthropod specimen collection by aspiration that occurs outside a building. + John Judkins + animal biting catch - outdoors + MIRO:30000014 + https://github.com/obi-ontology/obi/issues/1217 animal-biting outdoor arthropod specimen collection by aspiration @@ -76575,11 +81978,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre aquatic arthropod specimen collection process - An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. - John Judkins - aquatic environment catch - MIRO:30000048 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. + John Judkins + aquatic environment catch + MIRO:30000048 + https://github.com/obi-ontology/obi/issues/1217 aquatic arthropod specimen collection process @@ -76591,11 +81994,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod resting in animal house specimen collection by aspiration - An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. - John Judkins - animal shed resting catch - MIRO:30000027 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. + John Judkins + animal shed resting catch + MIRO:30000027 + https://github.com/obi-ontology/obi/issues/1217 arthropod resting in animal house specimen collection by aspiration @@ -76607,11 +82010,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod resting outdoors on artificial support specimen collection by aspiration - An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. - John Judkins - outdoors shelter catch - artificial - MIRO:30000026 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. + John Judkins + outdoors shelter catch - artificial + MIRO:30000026 + https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors on artificial support specimen collection by aspiration @@ -76623,11 +82026,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod resting outdoors on natural support specimen collection by aspiration - An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. - John Judkins - outdoors shelter catch - natural - MIRO:30000025 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. + John Judkins + outdoors shelter catch - natural + MIRO:30000025 + https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors on natural support specimen collection by aspiration @@ -76639,11 +82042,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod resting outdoors specimen collection by aspiration - An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. - John Judkins - outdoors shelter catch - MIRO:30000024 - https://github.com/obi-ontology/obi/issues/1217 + An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. + John Judkins + outdoors shelter catch + MIRO:30000024 + https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors specimen collection by aspiration @@ -76655,11 +82058,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod specimen collection by aspiration - A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. - John Judkins - catch by aspiration - MIRO:30000043 - https://github.com/obi-ontology/obi/issues/1217 + A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. + John Judkins + catch by aspiration + MIRO:30000043 + https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection by aspiration @@ -76671,12 +82074,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod specimen collection process - A specimen collection process that has the objective of collecting arthropods as specimens. - John Judkins - field population catch - collection of arthropods - MIRO:30000044 - https://github.com/obi-ontology/obi/issues/1217 + A specimen collection process that has the objective of collecting arthropods as specimens. + John Judkins + collection of arthropods + field population catch + MIRO:30000044 + https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection process @@ -76688,11 +82091,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre human-biting arthropod specimen collection by aspiration - An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. - John Judkins - man biting catch - MIRO:30000017 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. + John Judkins + man biting catch + MIRO:30000017 + https://github.com/obi-ontology/obi/issues/1217 human-biting arthropod specimen collection by aspiration @@ -76704,11 +82107,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre human-biting indoor arthropod specimen collection by aspiration - An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. - John Judkins - man biting catch - indoors - MIRO:30000019 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. + John Judkins + man biting catch - indoors + MIRO:30000019 + https://github.com/obi-ontology/obi/issues/1217 human-biting indoor arthropod specimen collection by aspiration @@ -76720,11 +82123,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre human-biting outdoor arthropod specimen collection by aspiration - An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. - John Judkins - man biting catch - outdoors - MIRO:30000018 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. + John Judkins + man biting catch - outdoors + MIRO:30000018 + https://github.com/obi-ontology/obi/issues/1217 human-biting outdoor arthropod specimen collection by aspiration @@ -76736,11 +82139,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre knockdown arthropod specimen collection by pyrethrum spray - A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. - John Judkins - pyrethrum spray catch - MIRO:30000023 - https://github.com/obi-ontology/obi/issues/1217 + A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. + John Judkins + pyrethrum spray catch + MIRO:30000023 + https://github.com/obi-ontology/obi/issues/1217 knockdown arthropod specimen collection by pyrethrum spray @@ -76752,11 +82155,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre knockdown arthropod specimen collection process - An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. - John Judkins - knockdown collection - IRO:0000014 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. + John Judkins + knockdown collection + IRO:0000014 + https://github.com/obi-ontology/obi/issues/1217 knockdown arthropod specimen collection process @@ -76768,12 +82171,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre live arthropod specimen collection process - An arthropod specimen collection process meant to collect live specimens. - John Judkins - catch of live specimens - VSMO:0001445 - MIRO:30000044 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod specimen collection process meant to collect live specimens. + John Judkins + catch of live specimens + MIRO:30000044 + VSMO:0001445 + https://github.com/obi-ontology/obi/issues/1217 live arthropod specimen collection process @@ -76785,10 +82188,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre arthropod trap - A device designed to catch arthropods. - John Judkins - MIRO:30000011 - https://github.com/obi-ontology/obi/issues/1217 + A device designed to catch arthropods. + John Judkins + MIRO:30000011 + https://github.com/obi-ontology/obi/issues/1217 arthropod trap @@ -76800,10 +82203,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre artificial pit shelter - An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. - John Judkins - IRO:0000005 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. + John Judkins + IRO:0000005 + https://github.com/obi-ontology/obi/issues/1217 artificial pit shelter @@ -76815,9 +82218,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre baited net trap - An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal. - John Judkins - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal. + John Judkins + https://github.com/obi-ontology/obi/issues/1217 baited net trap @@ -76829,10 +82232,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre barrier trap - An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. - John Judkins - IRO:0000017 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. + John Judkins + IRO:0000017 + https://github.com/obi-ontology/obi/issues/1217 barrier trap @@ -76850,10 +82253,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre BG-Counter - A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. - John Judkins - IRO:0000143 - https://github.com/obi-ontology/obi/issues/1217 + A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. + John Judkins + IRO:0000143 + https://github.com/obi-ontology/obi/issues/1217 BG-Counter @@ -76871,11 +82274,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre BG-Sentinel trap - An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current. - John Judkins - IRO:0000028 - VSMO:0001906 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current. + John Judkins + IRO:0000028 + VSMO:0001906 + https://github.com/obi-ontology/obi/issues/1217 BG-Sentinel trap @@ -76887,12 +82290,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Centers for Disease Control and Prevention light trap - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. - This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. - John Judkins - CDC light trap - IRO:0000163 - https://github.com/obi-ontology/obi/issues/1217 + A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. + This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. + John Judkins + CDC light trap + IRO:0000163 + https://github.com/obi-ontology/obi/issues/1217 Centers for Disease Control and Prevention light trap @@ -76904,11 +82307,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre dipper for arthropod immatures - A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. - John Judkins - dipper for immatures - VSMO:0001479 - https://github.com/obi-ontology/obi/issues/1217 + A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. + John Judkins + dipper for immatures + VSMO:0001479 + https://github.com/obi-ontology/obi/issues/1217 dipper for arthropod immatures @@ -76920,12 +82323,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre encephalitis virus surveillance trap - A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods. - John Judkins - EVS trap - IRO:0000029 - VSMO:0001295 - https://github.com/obi-ontology/obi/issues/1217 + A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods. + John Judkins + EVS trap + IRO:0000029 + VSMO:0001295 + https://github.com/obi-ontology/obi/issues/1217 encephalitis virus surveillance trap @@ -76937,10 +82340,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre gravid trap - An arthropod trap that is designed to collect gravid female arthropods or their eggs. - John Judkins - IRO:0000030 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that is designed to collect gravid female arthropods or their eggs. + John Judkins + IRO:0000030 + https://github.com/obi-ontology/obi/issues/1217 gravid trap @@ -76952,10 +82355,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre light trap - An arthropod trap that uses light as an attractant. - John Judkins - MIRO:30000065 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that uses light as an attractant. + John Judkins + MIRO:30000065 + https://github.com/obi-ontology/obi/issues/1217 light trap @@ -76967,11 +82370,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre light trap for indoor use - A light trap designed to be placed inside a building. - John Judkins - indoor light trap - MIRO:30000009 - https://github.com/obi-ontology/obi/issues/1217 + A light trap designed to be placed inside a building. + John Judkins + indoor light trap + MIRO:30000009 + https://github.com/obi-ontology/obi/issues/1217 light trap for indoor use @@ -76983,11 +82386,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre light trap for outdoor use - A light trap designed to be placed outside a building. - John Judkins - outdoor light trap - MIRO:30000010 - https://github.com/obi-ontology/obi/issues/1217 + A light trap designed to be placed outside a building. + John Judkins + outdoor light trap + MIRO:30000010 + https://github.com/obi-ontology/obi/issues/1217 light trap for outdoor use @@ -76999,10 +82402,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Mosquito Magnet trap - An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. - John Judkins - IRO:0000022 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. + John Judkins + IRO:0000022 + https://github.com/obi-ontology/obi/issues/1217 Mosquito Magnet trap @@ -77014,10 +82417,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre MosquiTRAP - A gravid trap consisting of an arthropod attractant and adhesive surface. - John Judkins - IRO:0000140 - https://github.com/obi-ontology/obi/issues/1217 + A gravid trap consisting of an arthropod attractant and adhesive surface. + John Judkins + IRO:0000140 + https://github.com/obi-ontology/obi/issues/1217 MosquiTRAP @@ -77029,11 +82432,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre New Jersey light trap - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. - John Judkins - New Jersey trap - IRO:0000031 - https://github.com/obi-ontology/obi/issues/1217 + A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. + John Judkins + New Jersey trap + IRO:0000031 + https://github.com/obi-ontology/obi/issues/1217 New Jersey light trap @@ -77045,12 +82448,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Onderstepoort Veterinary Institute light-suction trap - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter. - John Judkins - OVI light-suction trap - IRO:0000154 - Parasites Vectors 8, 239 (2015) - https://github.com/obi-ontology/obi/issues/1217 + A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter. + John Judkins + OVI light-suction trap + IRO:0000154 + Parasites Vectors 8, 239 (2015) + https://github.com/obi-ontology/obi/issues/1217 Onderstepoort Veterinary Institute light-suction trap @@ -77062,11 +82465,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre outlet window trap - An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. - John Judkins + An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. + John Judkins outlet window trap - MIRO:30000020 - https://github.com/obi-ontology/obi/issues/1217 + MIRO:30000020 + https://github.com/obi-ontology/obi/issues/1217 outlet window trap @@ -77078,12 +82481,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre ovitrap - An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females. - John Judkins - oviposition trap - MIRO:30000016 - VSMO:0001501 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females. + John Judkins + oviposition trap + MIRO:30000016 + VSMO:0001501 + https://github.com/obi-ontology/obi/issues/1217 ovitrap @@ -77095,9 +82498,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre resting arthropod trap - An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. - John Judkins - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. + John Judkins + https://github.com/obi-ontology/obi/issues/1217 resting arthropod trap @@ -77109,11 +82512,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre resting box trap - An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. - John Judkins - resting box catch - IRO:0000021 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. + John Judkins + resting box catch + IRO:0000021 + https://github.com/obi-ontology/obi/issues/1217 resting box trap @@ -77125,11 +82528,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre resting bucket - An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host). - John Judkins - resting bucket catch - IRO:0000141 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host). + John Judkins + resting bucket catch + IRO:0000141 + https://github.com/obi-ontology/obi/issues/1217 resting bucket @@ -77141,11 +82544,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Shannon trap - An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap. - John Judkins - shannon trap catch - IRO:0000191 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap. + John Judkins + shannon trap catch + IRO:0000191 + https://github.com/obi-ontology/obi/issues/1217 Shannon trap @@ -77157,11 +82560,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre sticky resting bucket - An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected. - John Judkins - sticky resting bucket catch - IRO:0000142 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected. + John Judkins + sticky resting bucket catch + IRO:0000142 + https://github.com/obi-ontology/obi/issues/1217 sticky resting bucket @@ -77173,11 +82576,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre sticky trap - An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. - John Judkins - sticky trap catch - IRO:0000128 - https://github.com/obi-ontology/obi/issues/1217 + An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. + John Judkins + sticky trap catch + IRO:0000128 + https://github.com/obi-ontology/obi/issues/1217 sticky trap @@ -77187,13 +82590,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - population based design + population based design - A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. - Chris Stoeckert - https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design - #1090 - population based design + A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. + Chris Stoeckert + https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design + #1090 + population based design @@ -77227,13 +82630,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based apoptosis assay - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/1 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/1 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based apoptosis assay @@ -77268,14 +82671,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based cell proliferation assay - A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - fluroescence imaging-based cell count assay - url:http://lincsportal.ccs.miami.edu/beta/assays/31 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + fluroescence imaging-based cell count assay + url:http://lincsportal.ccs.miami.edu/beta/assays/31 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based cell proliferation assay @@ -77310,13 +82713,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluroescence imaging-based cell cycle state assay - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/10 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/10 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluroescence imaging-based cell cycle state assay @@ -77351,13 +82754,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based cell viability assay - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/27 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/27 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based cell viability assay @@ -77392,13 +82795,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based drug synergy assay - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/7 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/7 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based drug synergy assay @@ -77433,15 +82836,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based cell morphology assay - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based cell morphology assay @@ -77476,13 +82879,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging multiplex cytological profiling - A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/8 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/8 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging multiplex cytological profiling @@ -77494,15 +82897,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre protein state assay - A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS protein state assay @@ -77537,13 +82940,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based protein phosphorylation state assay - A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/15 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/15 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based protein phosphorylation state assay @@ -77561,15 +82964,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre mass spectrometry-based protein state assay - A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS mass spectrometry-based protein state assay @@ -77581,15 +82984,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay - A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - P100 phosphoprotein quantification assay - PMID:26912667 - PMID:29655704 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + P100 phosphoprotein quantification assay + PMID:26912667 + PMID:29655704 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay @@ -77601,17 +83004,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre reverse phase protein array profiling assay - A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - RPLA assay - RPPA assay - reverse phase lysate array profiling assay - PMID: 17041095 - PMID:31820393 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + RPLA assay + RPPA assay + reverse phase lysate array profiling assay + PMID: 17041095 + PMID:31820393 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS reverse phase protein array profiling assay @@ -77629,14 +83032,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre SWATH-MS protein profiling assay - A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - sequential window acquisition of all theoretical mass spectra protein profiling assay - PMID:30104418 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sequential window acquisition of all theoretical mass spectra protein profiling assay + PMID:30104418 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS SWATH-MS protein profiling assay @@ -77646,16 +83049,16 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - tandem mass tag mass spectrometry + tandem mass tag mass spectrometry assay - A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:12713048 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - tandem mass tag mass spectrometry + A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:12713048 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + tandem mass tag mass spectrometry assay @@ -77689,15 +83092,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorescence imaging-based reporter gene assay - A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS fluorescence imaging-based reporter gene assay @@ -77721,16 +83124,16 @@ b) that the amount of analyte/measurand detected is over some predetermined thre global chromatin profiling by mass spectrometry assay - A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - GCP - global chromatin epigenetic profiling - global chromatin profiling - PMID:25448295 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + GCP + global chromatin epigenetic profiling + global chromatin profiling + PMID:25448295 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS global chromatin profiling by mass spectrometry assay @@ -77742,15 +83145,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre kinase inhibitor assay - A type of assay that identifies compounds that inhibit the activity of kinases. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of assay that identifies compounds that inhibit the activity of kinases. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS kinase inhibitor assay @@ -77762,13 +83165,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre KINOMEscan assay - A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS KINOMEscan assay @@ -77780,13 +83183,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre KiNativ assay - A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.kinativ.com/technology.html - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.kinativ.com/technology.html + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS KiNativ assay @@ -77798,14 +83201,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre landmark transcript profiling assay - A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - L1000 mRNA profiling assay - PMID:29195078 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + L1000 mRNA profiling assay + PMID:29195078 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS landmark transcript profiling assay @@ -77817,14 +83220,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre microenvironment microarray assay - A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - MEMA assay - PMID:29199020 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MEMA assay + PMID:29199020 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS microenvironment microarray assay @@ -77836,13 +83239,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre microwestern meso-scale quantitative western blot assay - A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:28092050 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:28092050 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS microwestern meso-scale quantitative western blot assay @@ -77860,14 +83263,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre positive/negative ion switching metabolite profiling assay - A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - positive/negative ion switching metabolomic assay - PMID:22498707 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + positive/negative ion switching metabolomic assay + PMID:22498707 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS positive/negative ion switching metabolite profiling assay @@ -77879,14 +83282,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cyclic immunoflouroescence assay - A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:27925668 - PMID:29993362 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:27925668 + PMID:29993362 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS cyclic immunoflouroescence assay @@ -77898,13 +83301,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre multiplex bead-based protein state immunoassay - A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS + A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS multiplex bead-based protein state immunoassay @@ -77931,9 +83334,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre endotracheal tube specimen - A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. - John Judkins ORCID:0000-0001-6595-0902 - https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. + John Judkins ORCID:0000-0001-6595-0902 + https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal tube specimen @@ -77960,9 +83363,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre endotracheal aspirate specimen - A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. - John Judkins ORCID:0000-0001-6595-0902 - https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. + John Judkins ORCID:0000-0001-6595-0902 + https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal aspirate specimen @@ -77973,13 +83376,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre input protein sequence start site - When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site. + When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site. - The position of the first amino acid in a protein sequence being analyzed (input protein sequence). - Emma Griffiths - input protein start - query protein start site - Emma Griffiths + The position of the first amino acid in a protein sequence being analyzed (input protein sequence). + Emma Griffiths + input protein start + query protein start site + Emma Griffiths input protein sequence start site @@ -77990,13 +83393,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre input protein sequence stop site - When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site. + When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site. - The position of the last amino acid in a protein sequence being analyzed (input protein sequence). - Emma Griffiths - input protein stop - query protein stop site - Emma Griffiths + The position of the last amino acid in a protein sequence being analyzed (input protein sequence). + Emma Griffiths + input protein stop + query protein stop site + Emma Griffiths input protein sequence stop site @@ -78007,13 +83410,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre input gene sequence start site - When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. + When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. - The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). - Emma Griffiths - input gene start - query gene start site - Emma Griffiths + The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). + Emma Griffiths + input gene start + query gene start site + Emma Griffiths input gene sequence start site @@ -78024,13 +83427,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre input gene sequence stop site - When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site. + When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site. - The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). - Emma Griffiths - input gene stop - query gene stop site - Emma Griffiths + The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). + Emma Griffiths + input gene stop + query gene stop site + Emma Griffiths input gene sequence stop site @@ -78041,13 +83444,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre reference protein sequence start site - When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site. + When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site. - The position of the first amino acid in a reference protein sequence (sequence being used for comparison). - Emma Griffiths - reference protein start - subject protein start site - Emma Griffiths + The position of the first amino acid in a reference protein sequence (sequence being used for comparison). + Emma Griffiths + reference protein start + subject protein start site + Emma Griffiths reference protein sequence start site @@ -78058,13 +83461,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre reference protein sequence stop site - When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site. + When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site. - The position of the last amino acid in a reference protein sequence (sequence being used for comparison). - Emma Griffiths - reference protein stop - subject protein stop site - Emma Griffiths + The position of the last amino acid in a reference protein sequence (sequence being used for comparison). + Emma Griffiths + reference protein stop + subject protein stop site + Emma Griffiths reference protein sequence stop site @@ -78075,13 +83478,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre reference gene sequence start site - When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site. + When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site. - The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). - Emma Griffiths - reference gene start - subject gene start site - Emma Griffiths + The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). + Emma Griffiths + reference gene start + subject gene start site + Emma Griffiths reference gene sequence start site @@ -78092,13 +83495,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre reference gene sequence stop site - When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site. + When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site. - The position of the last nucelotide in a reference sequence (sequence being used for comparison). - Emma Griffiths - reference gene stop - subject gene stop site - Emma Griffiths + The position of the last nucelotide in a reference sequence (sequence being used for comparison). + Emma Griffiths + reference gene stop + subject gene stop site + Emma Griffiths reference gene sequence stop site @@ -78123,13 +83526,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre capture Hi-C assay - PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. + PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. - A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. - Bonita Lam - cHi-C - PMID:29979818 - https://github.com/obi-ontology/obi/issues/1251 + A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. + Bonita Lam + cHi-C + PMID:29979818 + https://github.com/obi-ontology/obi/issues/1251 capture Hi-C assay @@ -78165,11 +83568,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre magnetic resonance imaging assay - An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. - Rebecca Jackson - MRI - url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging - https://github.com/obi-ontology/obi/issues/1290 + An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. + Rebecca Jackson + MRI + url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging + https://github.com/obi-ontology/obi/issues/1290 magnetic resonance imaging assay @@ -78205,13 +83608,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre computed tomography imaging assay - An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. - Rebecca Jackson - CAT scan - CT scan - computed tomography scan - url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 - https://github.com/obi-ontology/obi/issues/1290 + An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. + Rebecca Jackson + CAT scan + CT scan + computed tomography scan + url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 + https://github.com/obi-ontology/obi/issues/1290 computed tomography imaging assay @@ -78247,12 +83650,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre positron emission tomography imaging assay - An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. - Rebecca Jackson - PET scan - positron emission tomography scan - url:https://en.wikipedia.org/wiki/Positron_emission_tomography - https://github.com/obi-ontology/obi/issues/1290 + An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. + Rebecca Jackson + PET scan + positron emission tomography scan + url:https://en.wikipedia.org/wiki/Positron_emission_tomography + https://github.com/obi-ontology/obi/issues/1290 positron emission tomography imaging assay @@ -78309,11 +83712,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre T cell receptor repertoire sequencing assay - A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. - Rebecca Jackson - TCR repertoire sequencing assay - doi:10.1186/s12896-017-0379-9 - https://github.com/obi-ontology/obi/issues/1307 + A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. + Rebecca Jackson + TCR repertoire sequencing assay + doi:10.1186/s12896-017-0379-9 + https://github.com/obi-ontology/obi/issues/1307 T cell receptor repertoire sequencing assay @@ -78325,12 +83728,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre B cell receptor repertoire sequencing assay - A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. - Rebecca Jackson - Antibody repertoire sequencing assay - BCR repertoire sequencing assay - doi:10.1186/s12896-017-0379-9 - https://github.com/obi-ontology/obi/issues/1307 + A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. + Rebecca Jackson + Antibody repertoire sequencing assay + BCR repertoire sequencing assay + doi:10.1186/s12896-017-0379-9 + https://github.com/obi-ontology/obi/issues/1307 B cell receptor repertoire sequencing assay @@ -78641,9 +84044,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre ferritin assay - An assay that measures ferritin - James A. Overton, ORCID:0000-0001-5139-5557 - OBI + An assay that measures ferritin + James A. Overton, ORCID:0000-0001-5139-5557 + OBI ferritin assay @@ -78671,9 +84074,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fibrinogen assay - An assay that measures fibrinogen - James A. Overton, ORCID:0000-0001-5139-5558 - OBI + An assay that measures fibrinogen + James A. Overton, ORCID:0000-0001-5139-5558 + OBI fibrinogen assay @@ -78714,9 +84117,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre iron assay - An analyte assay that measures the abundance of iron - James A. Overton, ORCID:0000-0001-5139-5559 - OBI + An analyte assay that measures the abundance of iron + James A. Overton, ORCID:0000-0001-5139-5559 + OBI iron assay @@ -78757,9 +84160,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre ionized calcium assay - An analyte assay that measures the abundance of ionized calcium - James A. Overton, ORCID:0000-0001-5139-5561 - OBI + An analyte assay that measures the abundance of ionized calcium + James A. Overton, ORCID:0000-0001-5139-5561 + OBI ionized calcium assay @@ -78800,9 +84203,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre transferrin assay - An analyte assay that measures the abundance of transferrin - James A. Overton, ORCID:0000-0001-5139-5562 - OBI + An analyte assay that measures the abundance of transferrin + James A. Overton, ORCID:0000-0001-5139-5562 + OBI transferrin assay @@ -78843,9 +84246,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre uric acid assay - An analyte assay that measures the abundance of uric acid - James A. Overton, ORCID:0000-0001-5139-5563 - OBI + An analyte assay that measures the abundance of uric acid + James A. Overton, ORCID:0000-0001-5139-5563 + OBI uric acid assay @@ -78886,9 +84289,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre globulin assay - An analyte assay that measures the abundance of globulin - James A. Overton, ORCID:0000-0001-5139-5564 - OBI + An analyte assay that measures the abundance of globulin + James A. Overton, ORCID:0000-0001-5139-5564 + OBI globulin assay @@ -78916,9 +84319,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre myelocyte assay - A cytometry assay that measures the abundance and/or characteristics of myelocytes - James A. Overton, ORCID:0000-0001-5139-5565 - OBI + A cytometry assay that measures the abundance and/or characteristics of myelocytes + James A. Overton, ORCID:0000-0001-5139-5565 + OBI myelocyte assay @@ -78946,9 +84349,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre metamyelocyte assay - A cytometry assay that measures the abundance and/or characteristics of metamyelocytes - James A. Overton, ORCID:0000-0001-5139-5566 - OBI + A cytometry assay that measures the abundance and/or characteristics of metamyelocytes + James A. Overton, ORCID:0000-0001-5139-5566 + OBI metamyelocyte assay @@ -78976,9 +84379,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre hematocrit assay - A cytometry assay that measures the proportion of red blood cells - James A. Overton, ORCID:0000-0001-5139-5567 - OBI + A cytometry assay that measures the proportion of red blood cells + James A. Overton, ORCID:0000-0001-5139-5567 + OBI hematocrit assay @@ -79006,9 +84409,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre promyelocyte assay - A cytometry assay that measures the abundance and/or characteristics of promyelocytes - James A. Overton, ORCID:0000-0001-5139-5568 - OBI + A cytometry assay that measures the abundance and/or characteristics of promyelocytes + James A. Overton, ORCID:0000-0001-5139-5568 + OBI promyelocyte assay @@ -79036,9 +84439,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre basophil assay - A cytometry assay that measures the abundance and/or characteristics of basophils - James A. Overton, ORCID:0000-0001-5139-5569 - OBI + A cytometry assay that measures the abundance and/or characteristics of basophils + James A. Overton, ORCID:0000-0001-5139-5569 + OBI basophil assay @@ -79066,9 +84469,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre neutrophil assay - A cytometry assay that measures the abundance and/or characteristics of neutrophils - James A. Overton, ORCID:0000-0001-5139-5570 - OBI + A cytometry assay that measures the abundance and/or characteristics of neutrophils + James A. Overton, ORCID:0000-0001-5139-5570 + OBI neutrophil assay @@ -79096,9 +84499,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre eosinophil assay - A cytometry assay that measures the abundance and/or characteristics of eosinophils - James A. Overton, ORCID:0000-0001-5139-5571 - OBI + A cytometry assay that measures the abundance and/or characteristics of eosinophils + James A. Overton, ORCID:0000-0001-5139-5571 + OBI eosinophil assay @@ -79126,9 +84529,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre lymphocyte assay - A cytometry assay that measures the abundance and/or characteristics of lymphocytes - James A. Overton, ORCID:0000-0001-5139-5572 - OBI + A cytometry assay that measures the abundance and/or characteristics of lymphocytes + James A. Overton, ORCID:0000-0001-5139-5572 + OBI lymphocyte assay @@ -79156,9 +84559,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre monocyte assay - A cytometry assay that measures the abundance and/or characteristics of monocytes - James A. Overton, ORCID:0000-0001-5139-5573 - OBI + A cytometry assay that measures the abundance and/or characteristics of monocytes + James A. Overton, ORCID:0000-0001-5139-5573 + OBI monocyte assay @@ -79186,9 +84589,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre reticulocyte assay - A cytometry assay that measures the abundance and/or characteristics of reticulocytes - James A. Overton, ORCID:0000-0001-5139-5574 - OBI + A cytometry assay that measures the abundance and/or characteristics of reticulocytes + James A. Overton, ORCID:0000-0001-5139-5574 + OBI reticulocyte assay @@ -79216,9 +84619,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre macrophage assay - A cytometry assay that measures the abundance and/or characteristics of macrophages - James A. Overton, ORCID:0000-0001-5139-5577 - OBI + A cytometry assay that measures the abundance and/or characteristics of macrophages + James A. Overton, ORCID:0000-0001-5139-5577 + OBI macrophage assay @@ -79246,9 +84649,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre platelet assay - A cytometry assay that measures the abundance and/or characteristics of platelets - James A. Overton, ORCID:0000-0001-5139-5578 - OBI + A cytometry assay that measures the abundance and/or characteristics of platelets + James A. Overton, ORCID:0000-0001-5139-5578 + OBI platelet assay @@ -79302,11 +84705,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fluorogenic PCR assay - A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. - John Judkins - TaqMan - MIRO:20000102 - https://github.com/obi-ontology/obi/issues/1320 + A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. + John Judkins + TaqMan + MIRO:20000102 + https://github.com/obi-ontology/obi/issues/1320 fluorogenic PCR assay @@ -79324,14 +84727,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre genotyping by PCR assay - genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. - - A genotyping assay that uses polymerase chain reaction. - Chris Stoeckert, ORCID:0000-0002-5714-991X - Jie Zheng, ORCID:0000-0002-2999-0103 - VEuPathDB - https://github.com/obi-ontology/obi/issues/1348 - VEuPathDB + genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. + + A genotyping assay that uses polymerase chain reaction. + Chris Stoeckert, ORCID:0000-0002-5714-991X + Jie Zheng, ORCID:0000-0002-2999-0103 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1348 + VEuPathDB genotyping by PCR assay @@ -79343,14 +84746,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cleavage under targets and release using nuclease assay - A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CUT&RUN assay - url:https://elifesciences.org/articles/21856 - https://github.com/obi-ontology/obi/issues/1192 - bonitalam + A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&RUN assay + url:https://elifesciences.org/articles/21856 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam cleavage under targets and release using nuclease assay @@ -79362,14 +84765,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cleavage under targets and tagmentation - A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CUT&Tag assay - url:https://www.nature.com/articles/s41467-019-09982-5 - https://github.com/obi-ontology/obi/issues/1192 - bonitalam + A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&Tag assay + url:https://www.nature.com/articles/s41467-019-09982-5 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam cleavage under targets and tagmentation @@ -79380,12 +84783,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre coma severity assay - Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. + Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. - A physical examination of individual that has the objective to determine the severity of coma in a patient. - John Judkins - https://github.com/obi-ontology/obi/issues/1357 - John Judkins + A physical examination of individual that has the objective to determine the severity of coma in a patient. + John Judkins + https://github.com/obi-ontology/obi/issues/1357 + John Judkins coma severity assay @@ -79455,12 +84858,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Plasmodium gametocyte detection assay - An assay that detects Plasmodium gametocytes in a specimen. - Chris Stoeckert - Jie Zheng - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that detects Plasmodium gametocytes in a specimen. + Chris Stoeckert + Jie Zheng + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 Plasmodium gametocyte detection assay @@ -79531,12 +84934,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre malaria rapid diagnosis assay - An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. - Chris Stoeckert - Jie Zheng - malaria rapid diagnosis test - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. + Chris Stoeckert + Jie Zheng + malaria rapid diagnosis test + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 malaria rapid diagnosis assay @@ -79606,11 +85009,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre parasite detection assay - An assay that detects parasite in a specimen. - Chris Stoeckert - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that detects parasite in a specimen. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 parasite detection assay @@ -79680,11 +85083,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre feces microbiology assay - An assay that detects microorganisms in a feces specimen. - John Judkins - stool test for microorganisms - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that detects microorganisms in a feces specimen. + John Judkins + stool test for microorganisms + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 feces microbiology assay @@ -79735,10 +85138,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood assay - An assay that has a blood specimen as evaulant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that has a blood specimen as evaulant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 blood assay @@ -79785,10 +85188,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre falcivax rapid diagnostic test - A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 falcivax rapid diagnostic test @@ -79835,10 +85238,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre optimal-IT rapid diagnostic test - A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 optimal-IT rapid diagnostic test @@ -79889,10 +85292,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre urine assay - An assay that has a urine specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that has a urine specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 urine assay @@ -79910,10 +85313,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre parasite species identification by PCR assay - An organism identification assay that identifies the species of parasites by PCR. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An organism identification assay that identifies the species of parasites by PCR. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 parasite species identification by PCR assay @@ -79938,11 +85341,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre parasite detection by PCR assay - An assay that detects parasite in a specimen using PCR. - Chris Stoeckert - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 + An assay that detects parasite in a specimen using PCR. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 parasite detection by PCR assay @@ -79953,11 +85356,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre free-standing window trap - Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] + Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] - An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. - VEuPathDB - VSMO:0001649 + An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. + VEuPathDB + VSMO:0001649 free-standing window trap @@ -79975,10 +85378,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre BG-lure scent dispenser - A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. - VEuPathDB - BG-lure - IRO:0001060 + A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. + VEuPathDB + BG-lure + IRO:0001060 BG-lure scent dispenser @@ -79990,9 +85393,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre hand-held sweep net - A device that consists of a network of mesh and is designed to capture adult arthropods. - VEuPathDB - VSMO:0001522 + A device that consists of a network of mesh and is designed to capture adult arthropods. + VEuPathDB + VSMO:0001522 hand-held sweep net @@ -80003,12 +85406,12 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Centers for Disease Control and Prevention gravid trap - The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] + The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] - A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. - VEuPathDB - CDC gravid trap - VSMO:0001510 + A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. + VEuPathDB + CDC gravid trap + VSMO:0001510 Centers for Disease Control and Prevention gravid trap @@ -80020,11 +85423,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre egg specimen collection process - An arthropod specimen collection process in which the arthropods are in the embryo stage. - VEuPath - collection of eggs - MIRO:30000049 - https://github.com/obi-ontology/obi/issues/1322 + An arthropod specimen collection process in which the arthropods are in the embryo stage. + VEuPath + collection of eggs + MIRO:30000049 + https://github.com/obi-ontology/obi/issues/1322 egg specimen collection process @@ -80036,11 +85439,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre larval specimen collection process - An arthropod specimen collection process in which the arthropods are in the larval stage. - VEuPath - collection of larvae - MIRO:30000022 - https://github.com/obi-ontology/obi/issues/1322 + An arthropod specimen collection process in which the arthropods are in the larval stage. + VEuPath + collection of larvae + MIRO:30000022 + https://github.com/obi-ontology/obi/issues/1322 larval specimen collection process @@ -80052,11 +85455,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre pupal specimen collection process - An arthropod specimen collection process in which the arthropods are in the pupal stage. - VEuPath - collection of pupae - MIRO:30000050 - https://github.com/obi-ontology/obi/issues/1322 + An arthropod specimen collection process in which the arthropods are in the pupal stage. + VEuPath + collection of pupae + MIRO:30000050 + https://github.com/obi-ontology/obi/issues/1322 pupal specimen collection process @@ -80083,10 +85486,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood specimen in vacutainer - A blood specimen that is located in a vacutainer. - John Judkins - Vacutainer sample - VEuPathDB + A blood specimen that is located in a vacutainer. + John Judkins + Vacutainer sample + VEuPathDB blood specimen in vacutainer @@ -80113,11 +85516,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood specimen on filter paper - A blood specimen that is located on a filter paper. - Chris Stoeckert - Jie Zheng - Filter paper sample - Penn Group + A blood specimen that is located on a filter paper. + Chris Stoeckert + Jie Zheng + Filter paper sample + Penn Group blood specimen on filter paper @@ -80129,9 +85532,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre proportion mapped reads - A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. - John Judkins - VEuPathDB + A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. + John Judkins + VEuPathDB proportion mapped reads @@ -80348,78 +85751,5166 @@ b) that the amount of analyte/measurand detected is over some predetermined thre common name of organism - A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. + A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. + John Judkins + https://en.wikipedia.org/wiki/Common_name + common name of organism + + + + + + + + + age since birth at time of enrollment + + An age since birth measurement datum at the time of subject enrollment. + Jie Zheng + Penn Group + age since birth at time of enrollment + + + + + + + + + age since birth at time of visit + + An age since birth measurement datum at the time of a clinical visit. + Chris Stoeckert + Grant Dorsey + Jie Zheng + Shon Cade + Penn Group + age since birth at time of visit + + + + + + + + + entomological data item + + A data item that is about a collection of insects. + John Judkins + entomological measurement datum + VEuPathDB + entomological data item + + + + + + + + + temperature measurement datum + + A scalar measurement datum that is the result of measuring temperature. + John Judkins + VEuPathDB + temperature measurement datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organismal body temperature measurement assay + + An assay that detects body temperature of an organism. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + organismal body temperature measurement assay + + + + + + + + + extraction date + + A time measurement datum that specifies when some material was extracted from an input material. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + FLU, VEuPathDB + https://github.com/obi-ontology/obi/issues/1286 + extraction date + + + + + + + + + extraction duration time + + A time measurement datum that is the result of measuring the duration of an extraction process. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + Meredith Keybl, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + extraction duration time + + + + + + + + + specimen collection time post disease onset + + A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post disease onset + + + + + + + + + specimen collection time post infection + + A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB, EUPATH:0000613 + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post infection + + + + + + + + + laboratory postal address + + A postal address used as a directive to deliver something to a laboratory. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + laboratory address + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + laboratory postal address + + + + + + + + + laboratory-based population + Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) + + A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1370 + laboratory-based population + + + + + + + + + autofluorescence assay + + A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + intrinsic fluorescence assay + PMID:25578980 + url:https://en.wikipedia.org/wiki/Autofluorescence + https://github.com/obi-ontology/obi/issues/1393 + CFDE + autofluorescence assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + autofluorescence microscopy assay + + An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:25578980 + url:https://en.wikipedia.org/wiki/Autofluorescence + https://github.com/obi-ontology/obi/issues/1394 + CFDE + autofluorescence microscopy assay + + + + + + + + + bulk assay for transposase-accessible chromatin using sequencing + + An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + bulk ATAC-seq + PMID:24097267 + https://github.com/obi-ontology/obi/issues/1395 + CFDE + bulk assay for transposase-accessible chromatin using sequencing + + + + + + + + + bulk RNA-seq assay + + An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.biostars.org/p/458516/ + https://github.com/obi-ontology/obi/issues/1396 + CFDE + bulk RNA-seq assay + + + + + + + + + + + + + + + multiplexed fluorescent antibody imaging assay + + An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:29993362 + https://github.com/obi-ontology/obi/issues/1397 + CFDE + multiplexed fluorescent antibody imaging assay + + + + + + + + + Cell DIVE multiplexed imaging assay + + A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://cancerres.aacrjournals.org/content/80/16_Supplement/1448 + url:https://www.cytivalifesciences.co.kr/wp-content/uploads/2020/07/Cell-DIVE-Tech-Info-Sheet-CY11898-09Apr20-DF.pdf + https://github.com/obi-ontology/obi/issues/1398 + CFDE + Cell DIVE multiplexed imaging assay + + + + + + + + + co-detection by indexing assay + + A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CODEX + url:https://www.scilifelab.se/facilities/co-detection-by-indexing-codex/ + https://github.com/obi-ontology/obi/issues/1399 + CFDE + co-detection by indexing assay + + + + + + + + + + + + + + + fluorescence in-situ hybridization assay + + An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + FISH + url:https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization + https://github.com/obi-ontology/obi/issues/1400 + CFDE + fluorescence in-situ hybridization assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + decoding amplified targeted transcripts with fluorescence in situ hybridization assay + + A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + DARTFISH + url:http://genome-tech.ucsd.edu/ZhangLab/index.php/data/tech-dev/ + url:http://www.weizmann.ac.il/conferences/SCG2015/sites/conferences.SCG2015/files/scg_2015_abstractbook_online_version.pdf + url:https://escholarship.org/uc/item/5bq3128f + https://github.com/obi-ontology/obi/issues/1401 + CFDE + decoding amplified targeted transcripts with fluorescence in situ hybridization assay + + + + + + + + + imaging mass cytometry assay + + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + IMC + imaging CyTOF + PMID:31798587 + https://github.com/obi-ontology/obi/issues/1403 + CFDE + imaging mass cytometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + LC-MS + CHMO:0000524 + https://github.com/obi-ontology/obi/issues/1404 + CFDE + liquid chromatography mass spectrometry assay + + + + + + + + + lightsheet fluorescence microscopy assay + + A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/light-sheet-fluorescence-microscopy + https://github.com/obi-ontology/obi/issues/1405 + CFDE + lightsheet fluorescence microscopy assay + + + + + + + + + matrix assisted laser desorption ionization imaging mass spectrometry assay + + A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MALDI-IMS + url:http://purl.obolibrary.org/obo/CHMO_0000054 + https://github.com/obi-ontology/obi/issues/1406 + CFDE + matrix assisted laser desorption ionization imaging mass spectrometry assay + + + + + + + + + multiplexed ion beam imaging assay + + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MIBI + url:https://www.nature.com/articles/s41374-020-0417-4 + https://github.com/obi-ontology/obi/issues/1407 + CFDE + multiplexed ion beam imaging assay + + + + + + + + + nanospray desorption electrospray ionization assay + + A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + NanoDESI + url:https://pubmed.ncbi.nlm.nih.gov/20593081/ + https://github.com/obi-ontology/obi/issues/1408 + CFDE + nanospray desorption electrospray ionization assay + + + + + + + + + + + + + + + nanodroplet processing in one pot for trace samples assay + + A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + NanoPOTS + url:https://www.emsl.pnnl.gov/science/related-instrument/nanodroplet-processing-in-one-pot-for-trace-samples--nanopots-/1806 + https://github.com/obi-ontology/obi/issues/1409 + CFDE + nanodroplet processing in one pot for trace samples assay + + + + + + + + + periodic acid-Schiff staining assay + + A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PAS staining + url:https://microbenotes.com/periodic-acid-schiff-pas-staining/ + https://github.com/obi-ontology/obi/issues/1410 + CFDE + periodic acid-Schiff staining assay + + + + + + + + + single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing + + An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sciATACseq + url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300/ + https://github.com/obi-ontology/obi/issues/1411 + CFDE + single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing + + + + + + + + + single-cell combinatorial indexing RNA sequencing assay + + A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sciRNAseq + url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894354/ + https://github.com/obi-ontology/obi/issues/1412 + CFDE + single-cell combinatorial indexing RNA sequencing assay + + + + + + + + + sequential fluorescence in-situ hybridization assay + + A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + seqFISH + url:https://spatial.caltech.edu/seqfish/ + https://github.com/obi-ontology/obi/issues/1413 + CFDE + sequential fluorescence in-situ hybridization assay + + + + + + + + + slide-seq assay + + An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://science.sciencemag.org/content/363/6434/1463 + https://github.com/obi-ontology/obi/issues/1414 + CFDE + slide-seq assay + + + + + + + + + single-nucleus chromatin accessibility and mRNA expression sequencing assay + + A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + SNARE-seq + SNAREseq + url:https://www.nature.com/articles/s41587-019-0290-0 + https://github.com/obi-ontology/obi/issues/1416 + CFDE + single-nucleus chromatin accessibility and mRNA expression sequencing assay + + + + + + + + + single-nucleus RNA sequencing assay + + A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sNuc-seq + single nuclei RNA sequencing + snRNA-seq + EFO:0009809 + url:https://www.biocompare.com/Editorial-Articles/557506-Advantages-of-Single-Nucleus-RNA-Sequencing/ + https://github.com/obi-ontology/obi/issues/1415 + CFDE + single-nucleus RNA sequencing assay + + + + + + + + + gas chromatography mass spectrometry assay + + A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + GC-MS + url:http://purl.bioontology.org/ontology/MESH/D008401 + https://github.com/obi-ontology/obi/issues/1417 + CFDE + gas chromatography mass spectrometry assay + + + + + + + + + SOMAscan assay + + An analyte assay that uses aptamers to detect protein analytes in serum. + Bjoern Peters + Randi Vita + Rohloff JC, et al. Nucleic acid ligands with protein-like side chains: modified aptamers and their uses as diagnostic and therapeutic agents. Mol Ther Nucleic Acids. 2014;3:e201. + https://github.com/obi-ontology/obi/issues/1308 + ImmPort + SOMAscan assay + + + + + + + + + Olink assay + + A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR. + Bjoern Peters + Hector Guzman-Orozco + Randi Vita + https://www.olink.com/ + https://github.com/obi-ontology/obi/issues/1308 + ImmPort + Olink assay + + + + + + + + + + + + + + + + proximity extension assay + + An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. + Bjoern Peters + Hector Guzman-Orozco + Randi Vita + Bjoern Peters + https://github.com/obi-ontology/obi/issues/1308 + ImmPort + proximity extension assay + + + + + + + + + + + + + + + Illumina MiniSeq + Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 + + A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + PERSON: Bonita Lam + MiniSeq + url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html + Illumina MiniSeq + + + + + + + + + + + + + + + + + + + + antigen detection by cytometric bead array assay + + A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. + CMI-PB + CMI-PB + https://github.com/obi-ontology/obi/issues/1399 + antigen detection by cytometric bead array assay + + + + + + + + + + + + + + + + + + + + antibody detection by cytometric bead array assay + + A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. + CMI-PB + CMI-PB + https://github.com/obi-ontology/obi/issues/1399 + antibody detection by cytometric bead array assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3D molecular structure determination assay + + An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. + Bjoern Peters + Hector Guzman-Orozco + IEDB + https://github.com/obi-ontology/obi/issues/1380 + 3D molecular structure determination assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + electron-microscopy 3D molecular structure determination assay + + A 3D molecular structure determination assay that uses electron microscopy imaging. + Bjoern Peters + Hector Guzman-Orozco + IEDB + https://github.com/obi-ontology/obi/issues/1380 + electron-microscopy 3D molecular structure determination assay + + + + + + + + + + + + + + + + + + + + + + antigen:antibody complex + + A complex of molecular entitites which is the result of an antibody binding to an antigen. + Bjoern Peters + Hector Guzman-Orozco + IEDB + antigen:antibody complex + + + + + + + + + + + + + + + + + + + + + + epitope:MHC:TCR complex + + A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex. + Bjorne Peters + Hector Guzman-Orozco + IEDB + epitope:MHC:TCR complex + + + + + + + + + + + + + + + MHC:ligand complex + + A complex of molecular entities which is the result of a MHC molecule binding with a ligand. + Bjorne Peters + Hector Guzman-Orozco + IEDB + MHC:ligand complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3D cell structure determination assay + + A 3D structure determination assay that determines the 3-dimensional configuration of a cell. + Hector Guzman-Orozco + Patrick Ray + Hector Guzman-Orozco + Patrick Ray + https://github.com/obi-ontology/obi/issues/1364 + 3D cell structure determination assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 3D neural cell structure determination assay + + A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. + Hector Guzman-Orozco + Patrick Ray + Hector Guzman-Orozco + Patrick Ray + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + 3D neural cell structure determination assay + + + + + + + + + + + + + + + + + + + + + + + + + + neuron morphology assay + + A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. + Hector Guzman-Orozco + Patrick Ray + Patrick Ray + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + neuron morphology assay + + + + + + + + + + + + + + + + + + + + + + + + + + mosaicism with repeat frameshift genetic sparse labeling + + A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. + Patrick Ray + MORF genetic sparse labeling + https://biccn.org/teams/u01-yang + https://doi.org/10.1016/j.neuron.2020.07.019 + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + mosaicism with repeat frameshift genetic sparse labeling + + + + + + + + + neuron morphology reconstruction assay + + A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). + The representation of the morphology (3D structure) of a neuron can be a summary of various measurements relating to the dimensions of the neuron in question. + Hector Guzman-Orozco + Patrick Ray + http://doi.org/10.1101/675280 + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + neuron morphology reconstruction assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + B cell epitope assay + + An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. + IEDB + IEDB + B cell assay|any method + B cell epitope assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + T cell epitope assay + + An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. + IEDB + IEDB + T cell assay|any method + T cell epitope assay + + + + + + + + + chemical mutagenesis + 129/Sv male mice were injected with ENU and mated to C57BL/6 females. Their first-generation (G1) male progeny were again crossed to C57BL/6 females, and then backcrossed to one of their second-generation (G2) daughters to yield a third-generation (G3). PMID:18802465 + + A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen. + Equivalent to FlyBase "chemical" (FBcv:0000525) in the origin of mutation branch and Dd mutagenesis meth0d term chemical mutagenesis (DDMUMET:0000014). + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/25646611/ + chemical mutagenesis + + + + + + + + + irradiation mutagenesis + Groups of (101 x C3H)F1 hybrid male mice 11 weeks old were exposed to two different doses of 137Cs gamma rays. PMID:7035547 + + A form of random mutagenesis that produces a random mutation by exposing the organism to radiation. + Equivalent to FlyBase "irradiation" (FBcv:0000503) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + radiation induced mutagenesis + url:http://purl.obolibrary.org/obo/FBcv_0000503 + irradiation mutagenesis + + + + + + + + + directed mutagenesis + Exons 20 and 21 were targeted for deletion because they encode the signature and Walker B motifs of the first ATP-binding domain, elements that are known to be critical for ABCA1 function. PMID:15550377 + + An induced mutation in which a specific gene(s) or part of a gene(s) is altered. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://www.ncbi.nlm.nih.gov/books/NBK21878/def-item/A4754/ + directed mutagenesis + + + + + + + + + endonuclease mediated mutagenesis + We have generated a WMS mouse model with S236X mutation in ADAMTS10 which is similar to the R237X mutation identifiedin WMS patients using CRISPR-Cas9. PMID:30060141 + + A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene. + Equivalent to FlyBase term "site specific cleavage" (FBcv:0003007) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/28177771/ + endonuclease mediated mutagenesis + + + + + + + + + cas mediated mutagenesis + Briefly, to create Adar1 M249A/M249A mice, guide RNA targeting 5’-ACCTTCTGAGCCTCTTGACA-3’ was synthesized by using Gene Art Precisiong RNA Synthesis Kit (ThermoFisherScientific). Pronuclear-stage mouse embryos (CLEA Japan Inc., Tokyo, Japan) were electroporated to introduce Cas9 mRNA, the guide RNA and a single-stranded donor... PMID:33983932 + + An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome. + Equivalent (narrow match) to FlyBase term "CRISPR/Cas9" (FBcv:0003008, narrow match as the OBI term covers all forms of cas) in the origin of mutation branch and Dd mutagenesis method term "CRISPR/Cas9" (DDMUMET:0000025). + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + CRISPR mediated mutagenesis + CRISPR/cas mediated mutagenesis + url:https://pubmed.ncbi.nlm.nih.gov/28177771/ + cas mediated mutagenesis + + + + + + + + + TALEN mediated mutagenesis + We designed transcription activator-like effector nucleases (TALENs) and a single-stranded oligo (ssOligo) donor template to edit the endogenous Actb locus within the mouse genome. PMID:30012594 + + An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome. + Equivalent to FlyBase term "TALEN" (FBcv:0003009) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/23664777/ + TALEN mediated mutagenesis + + + + + + + + + zinc finger mediated mutagenesis + ZFN constructs targeting the third exon of the mouse Apoc2 gene were designed and synthetized by Sigma Aldrich... PMID:26574515 + + An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome. + Equivalent to FlyBase term "ZFN" (FBcv:0003239) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + ZFN mediated mutagenesis + url:https://pubmed.ncbi.nlm.nih.gov/23664777/ + zinc finger mediated mutagenesis + + + + + + + + + transgenic mutagenesis + Transgenic mice were then generated by pronuclear injection of either the mixed MoPrP-PS1 and MoPrP-APP or the bicistronic MoPrP–APP/IRES/PS1 expression cassettes into single cell embryos derived from F2 hybrids of C57BL/6J and C3H/HeJ mice... PMID:11337275 + + A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/23996268/ + transgenic mutagenesis + + + + + + + + + gene-trap mutagenesis + Constructs lacking a promoter and including a B3-galactosidase gene, or a reporter gene encoding a protein with both B3-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. PMID:1653172 + + A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/17877761/ + gene-trap mutagenesis + + + + + + + + + enhancer-trap mutagenesis + We generated several lines of enhancer trap mice carrying an enhancer detector cassette expressing Cre recombinase under the transcriptional control of the minimal promoter (129 base pairs) of the mouse Thy-1.2 gene. PMID:22492032 + + A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/17877761/ + enhancer-trap mutagenesis + + + + + + + + + targeted mutagenesis + To disrupt the mdr1a gene a 1.6 kb NheI genomic fragment containing exons 6 and 7 was replaced by a hygromycin phosphotransferase cassette in a targeting vector. PMID:7910522 + + A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination. + Equivalent to FlyBase term "gene targeting by homologous recombination" (FBcv:0000710) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + gene targeting by homologous recombination + url:https://pubmed.ncbi.nlm.nih.gov/23996268/ + targeted mutagenesis + + + + + + + + + transposon-induced mutagenesis + In order to achieve SB transposon-mediated mutagenesis in mice, we employed the gene trap scheme using a novel transposon vector, and we have generated a large number of mutant mice, approximately 30% of which displayed the phenotype. PMID:16880528 + + A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation. + Equivalent to FlyBase "transposable element activity" (FBcv:0000483) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/32050713/ + transposon-induced mutagenesis + + + + + + + + + + + + + + + categorical binding datum + + A binding datum that is expressed as a categorical value. + IEDB + qualitative binding datum + IEDB + categorical binding datum + + + + + + + + + quantitative binding datum + + A binding datum that is expressed using numbers. + IEDB + IEDB + quantitative binding datum + + + + + + + + + + + + + + + + + + + + + + + + + + EC50 binding datum + + A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). + Bjoern Peters + Hector Guzman-Orozco + IEDB + EC50 binding datum + + + + + + + + + + + + + + + + + + + + + + + + + + IC50 binding datum + + A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). + Bjoern Peters + Hector Guzman-Orozco + IEDB + IC50 binding datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring quantitative binding of a MHC:ligand complex + + An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output. + IEDB + IEDB + quantitative binding|binding assay + assay measuring quantitative binding of a MHC:ligand complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring quantitative binding of an antigen:antibody complex + + An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output. + IEDB + IEDB + quantitative binding|binding assay + assay measuring quantitative binding of an antigen:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring quantitative binding of an epitope:MHC:TCR complex + + An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output. + IEDB + IEDB + quantitative binding|binding assay + assay measuring quantitative binding of an epitope:MHC:TCR complex + + + + + + + + + albumin concentration assay + + An albumin assay that measures the concentration of albumin in a specimen. + James A. Overton + albumin concentration assay + + + + + + + + + basophil percentage assay + + A basophil assay that measures the percentage of basophils in a specimen. + James A. Overton + basophil percentage assay + + + + + + + + + + calcium cation concentration assay + + A calcium cation assay that measures the concentration of calcium cations in a specimen. + James A. Overton + calcium cation concentration assay + + + + + + + + + chloride concentration assay + + A chloride assay that measures the concentration of chloride in a specimen. + James A. Overton + chloride concentration assay + + + + + + + + + cholesterol concentration assay + + A cholesterol assay that measures the concentration of cholesterol in a specimen. + James A. Overton + cholesterol concentration assay + + + + + + + + + creatinine concentration assay + + A creatinine assay that measures the concentration of creatinine in a specimen. + James A. Overton + creatinine concentration assay + + + + + + + + + eosinophil percentage assay + + An eosinophil assay that measures the percentage of eosinophils in a specimen. + James A. Overton + eosinophil percentage assay + + + + + + + + + globulin concentration assay + + A globulin assay that measures the concentration of globulin in a specimen. + James A. Overton + globulin concentration assay + + + + + + + + + hemoglobin concentration assay + + A hemoglobin assay that measures the amount of hemoglobin in a specimen. + James A. Overton + hemoglobin concentration assay + + + + + + + + + high-density lipoprotein cholesterol concentration assay + + A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. + James A. Overton + high-density lipoprotein cholesterol concentration assay + + + + + + + + + iron concentration assay + + An iron assay that measures the concentration of iron cation in a specimen. + James A. Overton + iron concentration assay + + + + + + + + + low-density lipoprotein cholesterol concentration assay + + A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. + James A. Overton + low-density lipoprotein cholesterol concentration assay + + + + + + + + + lymphocyte percentage assay + + A lymphocyte assay that measures the percentage of lymphocytes in a specimen. + James A. Overton + lymphocyte percentage assay + + + + + + + + + metamyelocyte count assay + + A metamyelocyte assay that measures the number of metamyelocytes in a specimen. + James A. Overton + metamyelocyte count assay + + + + + + + + + metamyelocyte percentage assay + + A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. + James A. Overton + metamyelocyte percentage assay + + + + + + + + + methemoglobin percentage assay + + A methemoglobin assay that measures the percentage of methemoglobin in a specimen. + James A. Overton + methemoglobin percentage assay + + + + + + + + + monocyte percentage assay + + A monocyte assay that measures the percentage of monocytes in a specimen. + James A. Overton + monocyte percentage assay + + + + + + + + + myelocyte count assay + + A myelocyte assay that measures the number of myelocytes in a specimen. + James A. Overton + myelocyte count assay + + + + + + + + + neutrophil percentage assay + + A neutrophil assay that measures the percentage of neutrophils in a specimen. + James A. Overton + neutrophil percentage assay + + + + + + + + + phosphate ion concentration assay + + A phosphate ion assay that measures the concentration of phosphate ions in a specimen. + James A. Overton + phosphate ion concentration assay + + + + + + + + + potassium(1+) concentration assay + + A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. + James A. Overton + potassium(1+) concentration assay + + + + + + + + + reticulocyte percentage assay + + A reticulocyte assay that measures the percentage of reticulocytes in a specimen. + James A. Overton + reticulocyte percentage assay + + + + + + + + + sodium(1+) concentration assay + + A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. + James A. Overton + sodium(1+) concentration assay + + + + + + + + + thyroid stimulating hormone concentration assay + + A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. + James A. Overton + thyroid stimulating hormone concentration assay + + + + + + + + + triglyceride concentration assay + + A triglyceride assay that measures the concentration of triglycerides in a specimen. + James A. Overton + triglyceride concentration assay + + + + + + + + + 3,3',5'-triiodothyronine concentration assay + + A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. + James A. Overton + 3,3',5'-triiodothyronine concentration assay + + + + + + + + + fibrinogen concentration assay + + A fibrinogen assay that measures the concentration of fibrinogen in a specimen. + James A. Overton + fibrinogen concentration assay + + + + + + + + + free thyroxine concentration assay + + A thyroxine assay that measures the concentration of free thyroxine in a specimen. + James A. Overton + free thyroxine concentration assay + + + + + + + + + total thyroxine concentration assay + + A thyroxine assay that measures the concentration of total thyroxine in a specimen. + James A. Overton + total thyroxine concentration assay + + + + + + + + + direct bilirubin concentration assay + + A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. + James A. Overton + direct bilirubin concentration assay + + + + + + + + + indirect bilirubin concentration assay + + A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. + James A. Overton + indirect bilirubin concentration assay + + + + + + + + + total bilirubin concentration assay + + A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. + James A. Overton + total bilirubin concentration assay + + + + + + + + + mean cell hemoglobin assay + + A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. + James A. Overton + mean cell hemoglobin assay + + + + + + + + + mean cell hemoglobin concentration assay + + A hemoglobin assay that measures the concentration of hemoglobin in a specimen. + James A. Overton + mean cell hemoglobin concentration assay + + + + + + + + + mean platelet volume assay + + A platelet assay that measures the average volume of platelets in a specimen. + James A. Overton + mean platelet volume assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immature neutrophil count assay + + A neutrophil assay that measures the number of immature neutrophils in a specimen. + James A. Overton + immature neutrophil count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immature neutrophil percentage assay + + An neutrophil assay that measures the percentage of immature neutrophils in a specimen. + James A. Overton + immature neutrophil percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nucleated erythrocyte percentage assay + + An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. + James A. Overton + nucleated erythrocyte percentage assay + + + + + + + + + mean cell volume assay + + An erythrocyte assay that measures the average volume of erythrocytes in a specimen. + James A. Overton + mean cell volume assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + erythrocyte assay + + A cytometry assay that measures the abundance and/or characteristics of erythrocytes. + James A. Overton + erythrocyte assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + manual hematocrit assay + + A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. + James A. Overton + manual hematocrit assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + adiponectin assay + + An analyte assay that measures the abundance of adiponectin + James A. Overton + adiponectin assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + adiponectin concentration assay + + An adiponectin assay that measures the concentration of adiponectin in a specimen. + James A. Overton + adiponectin concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + creatine assay + + An analyte assay that measures the abundance of creatine + James A. Overton + creatine assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + creatine concentration assay + + A creatine assay that measures the concentration of creatine in a specimen. + James A. Overton + creatine concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estradiol assay + + An analyte assay that measures the abundance of estradiol + James A. Overton + estradiol assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estradiol concentration assay + + An estradiol assay that measures the concentration of estradiol in a specimen. + James A. Overton + estradiol concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + leptin assay + + An analyte assay that measures the abundance of leptin + James A. Overton + leptin assay + + + + + + + + + leptin concentration assay + + An leptin assay that measures the concentration of leptin in a specimen. + James A. Overton + leptin concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lipoprotein concentration assay + + An analyte assay that measures the abundance of lipoprotein + James A. Overton + lipoprotein concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + high-density lipoprotein concentration assay + + A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. + James A. Overton + high-density lipoprotein concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + low-density lipoprotein concentration assay + + A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. + James A. Overton + low-density lipoprotein concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + very-low-density lipoprotein concentration assay + + A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. + James A. Overton + very-low-density lipoprotein concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + luteinizing hormone assay + + An analyte assay that measures the abundance of luteinizing hormone + James A. Overton + luteinizing hormone assay + + + + + + + + + luteinizing hormone concentration assay + + A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. + James A. Overton + luteinizing hormone concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nitrite assay + + An analyte assay that measures the abundance of nitrite + James A. Overton + nitrite assay + + + + + + + + + nitrite concentration assay + + A nitrite assay that measures the concentration of nitrite in a specimen. + James A. Overton + nitrite concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + phospholipid assay + + An analyte assay that measures the abundance of phospholipid + James A. Overton + phospholipid assay + + + + + + + + + phospholipid concentration assay + + A phospholipid assay that measures the concentration of phospholipids in a specimen. + James A. Overton + phospholipid concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + progesterone assay + + An analyte assay that measures the abundance of progesterone + James A. Overton + progesterone assay + + + + + + + + + progesterone concentration assay + + A progesterone assay that measures the concentration of progesterone in a specimen. + James A. Overton + progesterone concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + testosterone assay + + An analyte assay that measures the abundance of testosterone + James A. Overton + testosterone assay + + + + + + + + + testosterone concentration assay + + A testosterone assay that measures the concentration of testosterone in a specimen. + James A. Overton + testosterone concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bile salt assay + + An analyte assay that measures the abundance of bile salt + James A. Overton + bile salt assay + + + + + + + + + bile salt concentration assay + + A bile salt assay that measures the concentration of bile salt in a specimen. + James A. Overton + bile salt concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fatty acid assay + + An analyte assay that measures the abundance of fatty acid + James A. Overton + fatty acid assay + + + + + + + + + free fatty acid concentration assay + + A fatty acid assay that measures the concentration of free fatty acids in a specimen. + James A. Overton + free fatty acid concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insulin assay + + An analyte assay that measures the abundance of insulin + James A. Overton + insulin assay + + + + + + + + + insulin concentration assay + + A insulin assay that measures the concentration of insulin in a specimen. + James A. Overton + insulin concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + follicle stimulating hormone assay + + An analyte assay that measures the abundance of follicle stimulating hormone + James A. Overton + follicle stimulating hormone assay + + + + + + + + + follicle stimulating hormone concentration assay + + A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. + James A. Overton + follicle stimulating hormone concentration assay + + + + + + + + + total lymphocyte count assay + + A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. + James A. Overton + total lymphocyte count assay + + + + + + + + + total lymphocyte percentage assay + + A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. + James A. Overton + total lymphocyte percentage assay + + + + + + + + + + + + + + + fluorescent immunospot assay + + A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies. + Hector Guzman-Orozco + FLUOROSPOT + https://en.wikipedia.org/wiki/ELISpot#Mechanism_of_FluoroSpot + https://github.com/obi-ontology/obi/issues/1414 + CMI-PB + fluorescent immunospot assay + + + + + + + + + + + + + + + plasma proteomics assay + + A proteomics profiling assay that detects proteins in a blood plasma specimen. + Hector Guzman-Orozco + CMI-PB + https://github.com/obi-ontology/obi/issues/1414 + CMI-PB + plasma proteomics assay + + + + + + + + + T cell activation induced marker assay + + A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. + Hector Guzman-Orozco + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955771/ + https://github.com/obi-ontology/obi/issues/1414 + CMI-PB + T cell activation induced marker assay + + + + + + + + + + + + + + + leukapheresis + + A blood harvesting process in which white blood cells are separated from a blood specimen. + Hector Guzman-Orozco + https://en.wikipedia.org/wiki/Leukapheresis + leukapheresis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cerebrospinal fluid assay + + An assay that has a cerebrospinal fluid specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + cerebrospinal fluid assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + endotracheal aspirate assay + + An assay that has an endotracheal aspirate specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + endotracheal aspirate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + induced sputum assay + + An assay that has an induced sputum specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + induced sputum assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lung assay + + An assay that has a lung specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + lung assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + milk assay + + An assay that has a milk specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + milk assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + feces assay + + An assay that has a feces specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + umbilical cord blood assay + + An assay that has an umbilical cord blood specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + umbilical cord blood assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + saliva assay + + An assay that has a saliva specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + saliva assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cerebrospinal fluid microbiology assay + + An organism identification assay that has a cerebrospinal fluid specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + cerebrospinal fluid microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + endotracheal tube aspirate microbiology assay + + An organism identification assay that has an endotracheal aspirate specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + endotracheal tube aspirate microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + induced sputum microbiology assay + + An organism identification assay that has an induced sputum specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + induced sputum microbiology assay + + + + + + + + + + + + + + + blood assay datum + + A data item that is the specified output of a blood assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + blood assay datum + + + + + + + + + + + + + + + blood microbiology datum + + An organism identification assay that is the specified output of a blood microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + blood microbiology datum + + + + + + + + + + + + + + + feces assay datum + + A data item that is the specified output of a feces assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + feces assay datum + + + + + + + + + + + + + + + feces microbiology datum + + An organism identification assay that is the specified output of a feces microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + feces microbiology datum + + + + + + + + + + + + + + + urine assay datum + + A data item that is the specified output of a urine assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + urine assay datum + + + + + + + + + + + + + + + urine microbiology datum + + An organism identification assay that is the specified output of a urine microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + urine microbiology datum + + + + + + + + + + + + + + + induced sputum assay datum + + A data item that is the specified output of a induced sputum assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + induced sputum assay datum + + + + + + + + + + + + + + + induced sputum microbiology datum + + An organism identification assay that is the specified output of an induced sputum microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + induced sputum microbiology datum + + + + + + + + + + + + + + + cerebrospinal fluid assay datum + + A data item that is the specified output of a cerebrospinal fluid assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + cerebrospinal fluid assay datum + + + + + + + + + + + + + + + cerebrospinal fluid microbiology datum + + An organism identification assay that is the specified output of a cerebrospinal fluid microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + cerebrospinal fluid microbiology datum + + + + + + + + + + + + + + + endotracheal aspirate assay datum + + An organism identification assay that is the specified output of an endotracheal aspirate assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + endotracheal aspirate assay datum + + + + + + + + + + + + + + + endotracheal tube aspirate microbiology datum + + An organism identification assay that is the specified output of an endotracheal tube aspirate microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + endotracheal tube aspirate microbiology datum + + + + + + + + + + + + + + + lung microbiology datum + + An organism identification assay that is the specified output of a lung microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + lung microbiology datum + + + + + + + + + + + + + + + nasopharyngeal or oropharyngeal swab microbiology datum + + An organism identification assay that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + nasopharyngeal or oropharyngeal swab microbiology datum + + + + + + + + + + + + + + + pleural fluid microbiology datum + + An organism identification assay that is the specified output of a pleural fluid microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + pleural fluid microbiology datum + + + + + + + + + + + + + + + umbilical cord blood assay datum + + An organism identification assay that is the specified output of an umbilical cord blood assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + umbilical cord blood assay datum + + + + + + + + + + + + + + + umbilical cord blood microbiology datum + + An organism identification assay that is the specified output of an umbilical cord blood microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + umbilical cord blood microbiology datum + + + + + + + + + + + + + + + bacteria in blood datum + + A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in blood datum + + + + + + + + + + + + + + + virus in blood datum + + A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in blood datum + + + + + + + + + + + + + + + eukaryota in blood datum + + A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in blood datum + + + + + + + + + + + + + + + bacteria in feces datum + + A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in feces datum + + + + + + + + + + + + + + + eukaryota in feces datum + + A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in feces datum + + + + + + + + + + + + + + + virus in feces datum + + A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in feces datum + + + + + + + + + + + + + + + eukaryota in urine datum + + A urine microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in urine datum + + + + + + + + + + + + + + + bacteria in induced sputum datum + + A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in induced sputum datum + + + + + + + + + + + + + + + eukaryota in induced sputum datum + + A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in induced sputum datum + + + + + + + + + + + + + + + virus in induced sputum datum + + A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in induced sputum datum + + + + + + + + + + + + + + + bacteria in endotracheal tube aspirate datum + + A endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in endotracheal tube aspirate datum + + + + + + + + + + + + + + + bacteria in lung datum + + A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in lung datum + + + + + + + + + + + + + + + eukaryota in lung datum + + A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in lung datum + + + + + + + + + + + + + + + virus in lung datum + + A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in lung datum + + + + + + + + + + + + + + + bacteria in nasopharyngeal or oropharyngeal swab datum + + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in nasopharyngeal or oropharyngeal swab datum + + + + + + + + + + + + + + + eukaryota in nasopharyngeal or oropharyngeal swab datum + + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in nasopharyngeal or oropharyngeal swab datum + + + + + + + + + + + + + + + virus in nasopharyngeal or oropharyngeal swab datum + + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in nasopharyngeal or oropharyngeal swab datum + + + + + + + + + + + + + + + bacteria in pleural fluid datum + + A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in pleural fluid datum + + + + + + + + + + + + + + + eukaryota in pleural fluid datum + + A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in pleural fluid datum + + + + + + + + + + + + + + + virus in pleural fluid datum + + A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in pleural fluid datum + + + + + + + + + + + + + + + eukaryota in umbilical cord blood datum + + A umbilical cord blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in umbilical cord blood datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lung microbiology assay + + An organism identification assay that has a lung specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + lung microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pleural fluid microbiology assay + + An organism identification assay that has a pleural fluid specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + pleural fluid microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + umbilical cord blood microbiology assay + + An organism identification assay that has an umbilical cord blood specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + umbilical cord blood microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nasopharyngeal or oropharyngeal swab microbiology assay + + An organism identification assay that has a nasopharyngeal or oropharyngeal swab specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + nasopharyngeal or oropharyngeal swab microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine microbiology assay + + An organism identification assay that has a urine specimen as evaluant. John Judkins - https://en.wikipedia.org/wiki/Common_name - common name of organism - - - - - - - - - age since birth at time of enrollment - - An age since birth measurement datum at the time of subject enrollment. - Jie Zheng - Penn Group - age since birth at time of enrollment + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + urine microbiology assay - + - - - age since birth at time of visit + + + multiplex real time polymerase chain reaction assay - An age since birth measurement datum at the time of a clinical visit. - Chris Stoeckert - Grant Dorsey - Jie Zheng - Shon Cade - Penn Group - age since birth at time of visit + A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. + John Judkins + multiplexed real time polymerase chain reaction assay + VEuPathDB + https://github.com/obi-ontology/obi/issues/1431 + multiplex real time polymerase chain reaction assay - + - - - entomological data item + + + multiplex real time reverse-transcription polymerase chain reaction assay - A data item that is about a collection of insects. + A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. John Judkins - entomological measurement datum + multiplexed real time reverse-transcription polymerase chain reaction assay VEuPathDB - entomological data item + https://github.com/obi-ontology/obi/issues/1431 + multiplex real time reverse-transcription polymerase chain reaction assay - + - - - temperature measurement datum + + + mosquito membrane feeding device - A scalar measurement datum that is the result of measuring temperature. + A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. John Judkins VEuPathDB - temperature measurement datum + https://github.com/obi-ontology/obi/issues/1439 + mosquito membrane feeding device - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -80431,7 +90922,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -80442,7 +90933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -80454,128 +90945,220 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - organismal body temperature measurement assay - - An assay that detects body temperature of an organism. - Chris Stoeckert - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - organismal body temperature measurement assay - - - - - - - - - extraction date + + + + + + + + + + + + + + + + + + + + + + + + + mosquito membrane feeding assay + Testing the effectiveness of drugs or antibodies against parasite transmission. - A time measurement datum that specifies when some material was extracted from an input material. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - FLU, VEuPathDB - https://github.com/obi-ontology/obi/issues/1286 - extraction date + An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1439 + mosquito membrane feeding assay - + - - - extraction duration time + + + in silico design - A time measurement datum that is the result of measuring the duration of an extraction process. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - Meredith Keybl, Shane Babcock - https://github.com/obi-ontology/obi/issues/1286 - extraction duration time + A study design that is executed primarily on a computer. + Hector Guzman-Orozco + https://en.wikipedia.org/wiki/In_silico + https://github.com/obi-ontology/obi/issues/1430 + CMI-PB + in silico design - + - - - specimen collection time post disease onset + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granulysin release by T cells - A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - GROUP:FLU, Shane Babcock - https://github.com/obi-ontology/obi/issues/1286 - specimen collection time post disease onset + A cytometric bead array assay that detects granulysin release by T cells. + IEDB + IEDB + granulysin release|cytometric bead array + cytometric bead array assay measuring epitope specific granulysin release by T cells - + - - - specimen collection time post infection + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific perforin release by T cells - A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - VEuPathDB, EUPATH:0000613 - https://github.com/obi-ontology/obi/issues/1286 - specimen collection time post infection + A cytometric bead array assay that detects perforin release by T cells. + IEDB + IEDB + perforin release|cytometric bead array + cytometric bead array assay measuring epitope specific perforin release by T cells - + - - - laboratory postal address + + + + + + + + + modified acid-fast stain microscopy assay - A postal address used as a directive to deliver something to a laboratory. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - laboratory address - GROUP:FLU, Shane Babcock - https://github.com/obi-ontology/obi/issues/1286 - laboratory postal address + A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. + John Judkins + NCIT:C85736 + https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html + https://github.com/obi-ontology/obi/issues/1444 + modified acid-fast stain microscopy assay - + - - - laboratory-based population - Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) + + + positive binding datum - A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - VEuPathDB - https://github.com/obi-ontology/obi/issues/1370 - laboratory-based population + A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. + Bjoern Peters + Hector Guzman-Orozco + IEDB + positive binding datum - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Illumina MiniSeq - Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 + antibodies from lymphocyte secretions assay + PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. - A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. - PERSON: Bonita Lam - MiniSeq - url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html - Illumina MiniSeq + An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. + John Judkins + ALS assay + antibodies from lymphocyte supernatant assay + OBI + VEuPathDB + https://github.com/obi-ontology/obi/issues/1443 + antibodies from lymphocyte secretions assay @@ -80584,13 +91167,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - injection function + injection function - The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - adapted from WEB: http://www.dictionary.net/injection - injection function + The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + adapted from WEB: http://www.dictionary.net/injection + injection function @@ -80627,8 +91210,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch Epstein Barr virus transformed B cell @@ -80653,13 +91236,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre obsolete_anatomical entity - Tissue, organ, system, sperm, blood or body location (arm). + Tissue, organ, system, sperm, blood or body location (arm). - An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' - Bjoern Peters - Philippe Rocca-Serra - Tina Boussard - MO + An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' + Bjoern Peters + Philippe Rocca-Serra + Tina Boussard + MO obsolete_anatomical entity true @@ -80705,7 +91288,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. PERSON: Maura Gasparetto PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra plasma WEB: http://en.wikipedia.org/wiki/Blood_plasma blood plasma specimen @@ -80751,7 +91334,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen @@ -80779,11 +91362,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism @@ -80795,11 +91378,11 @@ This issue is outside the scope of OBI. obsolete_immortal cell - a single Hela cell + a single Hela cell - a cell derived from a multicellular organism that has the potential to replicate indefinitely - PERSON: Bjoern Peters - GROUP: OBI Biomaterial Branch + a cell derived from a multicellular organism that has the potential to replicate indefinitely + PERSON: Bjoern Peters + GROUP: OBI Biomaterial Branch obsolete_immortal cell true @@ -80812,11 +91395,11 @@ This issue is outside the scope of OBI. obsolete_fragment derived from protein - the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme + the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme - A material entity which is derived from a protein - PERSON: Bjoern Peters - GROUP: IEDB + A material entity which is derived from a protein + PERSON: Bjoern Peters + GROUP: IEDB obsolete_fragment derived from protein true @@ -80871,7 +91454,7 @@ This issue is outside the scope of OBI. Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra PERSON: Tina Boussard PBS buffer WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline @@ -80896,12 +91479,12 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - PERSON: James Malone - PERSON: Philippe Rocca-Serra + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen @@ -80914,9 +91497,9 @@ This issue is outside the scope of OBI. obsolete_cell line cell - A material entity that represents generations of a primary culture. - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch + A material entity that represents generations of a primary culture. + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch obsolete_cell line cell true @@ -80930,11 +91513,11 @@ This issue is outside the scope of OBI. obsolete_immortal cell line culture - A cell line that is expected to be capable of indefinite propagation in an vitro culture. - PERSON:Matthew Brush - immortal cell line sample - permanent cell line - PERSON:Matthew Brush + A cell line that is expected to be capable of indefinite propagation in an vitro culture. + PERSON:Matthew Brush + immortal cell line sample + permanent cell line + PERSON:Matthew Brush obsolete_immortal cell line culture @@ -80964,7 +91547,7 @@ This issue is outside the scope of OBI. A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra xenotransplant WEB: http://en.wikipedia.org/wiki/Xenograft xenograft @@ -80994,18 +91577,18 @@ This issue is outside the scope of OBI. - cultured cell population + cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). - A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. + A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. - PERSON:Matthew Brush + PERSON:Matthew Brush cell culture sample - PERSON:Matthew Brush - The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. - cultured cell population + PERSON:Matthew Brush + The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. + cultured cell population @@ -81033,18 +91616,18 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - primary cultured cell population - Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 - cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) + primary cultured cell population + Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 + cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) - A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. + A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' - PERSON:Matthew Brush - primary cell culture - primary cell culture sample - PERSON:Matthew Brush + PERSON:Matthew Brush + primary cell culture + primary cell culture sample + PERSON:Matthew Brush primary cultured cell population @@ -81067,13 +91650,13 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from obsolete_cell line - A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. - He, Tong-Chuan, et al. "Identification of c-MYC as a target of the APC pathway." Science 281.5382 (1998): 1509-1512. - "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'." + A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. + He, Tong-Chuan, et al. "Identification of c-MYC as a target of the APC pathway." Science 281.5382 (1998): 1509-1512. - "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'." - A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). - PERSON:Matthew Brush - cell line sample - OBI-CLO Alignment Working Group (Spring 2013) + A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). + PERSON:Matthew Brush + cell line sample + OBI-CLO Alignment Working Group (Spring 2013) obsolete_cell line @@ -81091,10 +91674,10 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. - PERSON: Susanna Sansone - PERSON:Matthew Brush + PERSON: Susanna Sansone + PERSON:Matthew Brush clonal cell culture sample - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch cultured clonal cell population @@ -81111,8 +91694,8 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application change biomaterial to material in definition PERSON: Bjoern Peters - GROUP: IEDB - 7/13/09: Need to clarify if this meets reagent role definition + GROUP: IEDB + 7/13/09: Need to clarify if this meets reagent role definition screening library @@ -81178,9 +91761,9 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra GROUP: CEBS - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch organ section @@ -81220,10 +91803,10 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ obsolete_polymer - A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - James Malone - Philippe Rocca-Serra - TERM: CHEBI:33839 + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + James Malone + Philippe Rocca-Serra + TERM: CHEBI:33839 obsolete_polymer true @@ -81241,13 +91824,13 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - glucose in solution - Glucose present in blood + glucose in solution + Glucose present in blood - A scattered aggregate of glucose molecules in a liquid - PERSON: Jie Zheng - glucose molecules - glucose in solution + A scattered aggregate of glucose molecules in a liquid + PERSON: Jie Zheng + glucose molecules + glucose in solution @@ -81291,14 +91874,14 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard @@ -81427,7 +92010,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. - Elisabetta Manduchi + Elisabetta Manduchi James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective @@ -81654,7 +92237,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra WEB: http://mathworld.wolfram.com/Cosine.html cosine transformation @@ -81721,7 +92304,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra PMID: 16646782 linlog transformation @@ -81762,7 +92345,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess global transformation @@ -81779,7 +92362,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess group transformation @@ -81832,7 +92415,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Helen Parkinson James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation single @@ -81855,7 +92438,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation paired @@ -81915,7 +92498,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra mean centring PERSON: Elisabetta Manduchi mean centering @@ -81938,7 +92521,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra median centring PERSON: Elisabetta Manduchi median centering @@ -81973,9 +92556,9 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ K-fold cross validation method - K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used - Person:Helen Parkinson - Tina Boussard + K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used + Person:Helen Parkinson + Tina Boussard K-fold cross validation method @@ -81992,11 +92575,11 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ leave one out cross validation method - The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 + The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 - is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 - Person:Helen Parkinson + is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 + Person:Helen Parkinson leave one out cross validation method @@ -82012,13 +92595,13 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - jackknifing method - simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure + jackknifing method + simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure - Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method - Helen Parkinson + Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method + Helen Parkinson jackknifing - http://en.wikipedia.org/wiki/Resampling_%28statistics%29 + http://en.wikipedia.org/wiki/Resampling_%28statistics%29 jackknifing method @@ -82035,11 +92618,11 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ boostrapping - Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. + Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient - Helen Parkinson - Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points + Helen Parkinson + Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points boostrapping @@ -82074,14 +92657,14 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Benjamini and Hochberg false discovery rate correction method - Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) + Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) - A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate + A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing - Helen Parkinson + Helen Parkinson Philippe Rocca-Serra - Helen Parkinson + Helen Parkinson Benjamini and Hochberg false discovery rate correction method @@ -82151,9 +92734,9 @@ specified input and output of dt which were missing k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). - Elisabetta Manduchi + Elisabetta Manduchi James Malone - Philippe Rocca-Serra + Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering @@ -82224,7 +92807,7 @@ specified input and output of dt which were missing single linkage hierarchical clustering A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster. - Elisabetta Manduchi + Elisabetta Manduchi PERSON: Elisabetta Manduchi single linkage hierarchical clustering @@ -82260,14 +92843,14 @@ specified input and output of dt which were missing Benjamini and Yekutieli false discovery rate correction method - The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) + The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) - A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate + A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing - Helen Parkinson + Helen Parkinson Philippe Rocca-Serra - Helen Parkinson + Helen Parkinson Benjamini and Yekutieli false discovery rate correction method @@ -82298,8 +92881,8 @@ specified input and output of dt which were missing Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra - data projection + Philippe Rocca-Serra + data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot @@ -82318,7 +92901,7 @@ specified input and output of dt which were missing Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone @@ -82410,7 +92993,7 @@ specified input and output of dt which were missing A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. Elisabetta Manduchi Helen Parkinson - Philippe Rocca-Serra + Philippe Rocca-Serra PERSON: Elisabetta Manduchi PERSON: Helen Parkinson moving average @@ -82528,7 +93111,7 @@ specified input and output of dt which were missing continuum mass spectrum A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. - PERSON: James Malone + PERSON: James Malone PERSON: Tina Hernandez-Boussard PERSON: Tina Boussard continuum mass spectrum @@ -82570,8 +93153,8 @@ specified input and output of dt which were missing A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data. Person:Tina Hernandez-Boussard - centroid mass spectrum calculation - centroiding + centroid mass spectrum calculation + centroiding centroid mass spectrum centroid mass spectrum @@ -82601,16 +93184,16 @@ specified input and output of dt which were missing Holm-Bonferroni family-wise error rate correction method - t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179 + t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179 - a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction + a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction 2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed - Person:Helen Parkinson + Person:Helen Parkinson Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method + WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method Holm-Bonferroni family-wise error rate correction method @@ -82648,7 +93231,7 @@ TO BE DEALT WITH STILL BY RICHARD. JAMES Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess transformation @@ -82704,14 +93287,14 @@ TO BE DEALT WITH STILL BY RICHARD. JAMES family wise error rate correction method - A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. + A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt - Monnie McGee + Monnie McGee Philippe Rocca-Serra FWER correction - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 family wise error rate correction method @@ -82874,7 +93457,7 @@ allows correct classification of FWER dt An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. James Malone Monnie McGee - Philippe Rocca-Serra + Philippe Rocca-Serra PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008) @@ -82891,7 +93474,7 @@ allows correct classification of FWER dt A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. Richard Scheuermann - network topology analysis + network topology analysis PERSON: Richard Scheuermann network analysis @@ -82905,8 +93488,8 @@ allows correct classification of FWER dt sequence analysis objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. - James Malone - PERSON: James Malone + James Malone + PERSON: James Malone sequence analysis objective @@ -82922,12 +93505,12 @@ allows correct classification of FWER dt - longitudinal data analysis + longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. - PERSON: James Malone - PERSON: Tina Boussard - correlation analysis + PERSON: James Malone + PERSON: Tina Boussard + correlation analysis longitudinal data analysis longitudinal data analysis @@ -82939,13 +93522,13 @@ allows correct classification of FWER dt survival analysis objective - Kaplan meier data transformation + Kaplan meier data transformation - A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables - PERSON: James Malone - PERSON: Tina Boussard - survival analysis - http://en.wikipedia.org/wiki/Survival_analysis + A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables + PERSON: James Malone + PERSON: Tina Boussard + survival analysis + http://en.wikipedia.org/wiki/Survival_analysis survival analysis objective @@ -82963,7 +93546,7 @@ allows correct classification of FWER dt mass spectrometry analysis - A data transformation which has the objective of spectrum analysis. + A data transformation which has the objective of spectrum analysis. mass spectrometry analysis @@ -82983,7 +93566,7 @@ allows correct classification of FWER dt A spread calculation is a data transformation that has objective spread calculation. James Malone - EDITOR + EDITOR spread calculation data transformation @@ -83001,10 +93584,10 @@ allows correct classification of FWER dt Kaplan Meier - a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) - PERSON: James Malone - PERSON: Tina Boussard - http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator + a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) + PERSON: James Malone + PERSON: Tina Boussard + http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator Kaplan Meier @@ -83020,12 +93603,12 @@ allows correct classification of FWER dt - multiple testing correction method + multiple testing correction method - A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate - Monnie McGee + A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate + Monnie McGee multiple testing procedure - PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. + PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method @@ -83035,16 +93618,16 @@ allows correct classification of FWER dt - inter-rater reliability objective - A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. + inter-rater reliability objective + A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. - a data transformation objective of determining the concordance or agreement between human judges. - Person:Alan Ruttenberg - Person:Helen Parkinson - inter-rater agreement - http://en.wikipedia.org/wiki/Inter-rater_reliability + a data transformation objective of determining the concordance or agreement between human judges. + Person:Alan Ruttenberg + Person:Helen Parkinson + inter-rater agreement + http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater reliability objective @@ -83074,11 +93657,11 @@ Examples include joint-probability of agreement, Cohen's kappa and the rela Westfall and Young family wise error rate correction - Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing + Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing 2011-03-31: [PRS]. specified input and output of dt which were missing PRS: 2011-03-31: set specified input and specified output to the data transformation - Helen Parkinson + Helen Parkinson Westfall and Young FWER correction Westfall and Young family wise error rate correction @@ -83146,11 +93729,11 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - non-negative matrix factorization - Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. + non-negative matrix factorization + Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. - Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. - http://en.wikipedia.org/wiki/Non-negative_matrix_factorization + Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. + http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization @@ -83166,7 +93749,7 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - soft independent modeling of class analogy analysis + soft independent modeling of class analogy analysis Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. Tina Hernandez-Boussard @@ -83370,10 +93953,10 @@ In this equation b0 is the regression coefficient for the intercept and the bi v partial least square discriminant analysis - PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. + PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. James Malone PLS-DA - WEB: http://www.camo.com/rt/Resources/pls-da.html + WEB: http://www.camo.com/rt/Resources/pls-da.html partial least square discriminant analysis @@ -83499,21 +94082,21 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - data visualization - Generation of a heatmap from a microarray dataset + data visualization + Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard - data encoding as image + data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard - Possible future hierarchy might include this: + Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding @@ -83593,7 +94176,7 @@ information_encoding A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). Monnie McGee - Philippe Rocca-Serra + Philippe Rocca-Serra ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. loess fitting @@ -83861,7 +94444,7 @@ information_encoding A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. Richard Scheuermann - data pooling + data pooling editor data combination @@ -84068,12 +94651,12 @@ information_encoding - mathematical feature + mathematical feature feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) James Malone - PERSON: James Malone + PERSON: James Malone mathematical feature @@ -84089,13 +94672,13 @@ information_encoding - log base + log base - The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. - Elisabetta Manduchi - logarithm base - logarithmic base - WEB: http://en.wikipedia.org/wiki/Logarithm + The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. + Elisabetta Manduchi + logarithm base + logarithmic base + WEB: http://en.wikipedia.org/wiki/Logarithm log base @@ -84197,14 +94780,14 @@ information_encoding - MA transformation - MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. + MA transformation + MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. - An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. - Elisabetta Manduchi - Philippe Rocca-Serra - PERSON: Elisabetta Manduchi - MA transformation + An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. + Elisabetta Manduchi + Philippe Rocca-Serra + PERSON: Elisabetta Manduchi + MA transformation @@ -84219,11 +94802,11 @@ information_encoding - exponential base + exponential base - The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). - Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Exponential_function + The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). + Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Exponential_function exponential base @@ -84239,11 +94822,11 @@ information_encoding - polynomial degree + polynomial degree - The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi + The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi polynomial degree @@ -84259,11 +94842,11 @@ information_encoding - number of variables + number of variables - The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi + The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi number of variables @@ -84276,9 +94859,9 @@ information_encoding agglomerative hierarchical clustering An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - bottom-up hierarchical clustering + bottom-up hierarchical clustering PERSON: Elisabetta Manduchi agglomerative hierarchical clustering @@ -84292,9 +94875,9 @@ information_encoding divisive hierarchical clustering A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - top-down hierarchical clustering + top-down hierarchical clustering PERSON: Elisabetta Manduchi divisive hierarchical clustering @@ -84324,7 +94907,7 @@ information_encoding data vector reduction objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. - James Malone + James Malone Richard H. Scheuermann PERSON: Richard H. Scheuermann data vector reduction objective @@ -84344,10 +94927,10 @@ information_encoding generalized family wise error rate correction method - A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. - Monnie McGee + A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. + Monnie McGee gFWER correction - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 generalized family wise error rate correction method @@ -84374,10 +94957,10 @@ information_encoding quantile number of false positives correction method - A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' - Monnie McGee + A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' + Monnie McGee QNFP - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 quantile number of false positives correction method @@ -84395,10 +94978,10 @@ information_encoding tail probability for the proportion of false positives correction method - A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. - Monnie McGee + A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. + Monnie McGee TPPFP correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 tail probability for the proportion of false positives correction method @@ -84429,14 +95012,14 @@ information_encoding false discovery rate correction method - The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . + The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt - Monnie McGee + Monnie McGee Philippe Rocca-Serra FDR correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate false discovery rate correction method @@ -84463,10 +95046,10 @@ allows correct classification of FDR dt proportion of expected false positives correction method - A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. - Monnie McGee + A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. + Monnie McGee PEFP correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 proportion of expected false positives correction method @@ -84493,10 +95076,10 @@ allows correct classification of FDR dt quantile proportion of false positives correction method - A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). - Monnie McGee + A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). + Monnie McGee QPFP correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 quantile proportion of false positives correction method @@ -84528,11 +95111,11 @@ allows correct classification of FDR dt A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. - Elisabetta Manduchi - Helen Parkinson + Elisabetta Manduchi + Helen Parkinson James Malone - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson PERSON: James Malone data normalization objective @@ -84548,8 +95131,8 @@ to create a common base for comparisons. A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone - PERSON: James Malone - PERSON: Melanie Courtot + PERSON: James Malone + PERSON: Melanie Courtot correction objective @@ -84576,7 +95159,7 @@ to create a common base for comparisons. normalization data transformation A normalization data transformation is a data transformation that has objective normalization. - James Malone + James Malone PERSON: James Malone normalization data transformation @@ -84604,7 +95187,7 @@ to create a common base for comparisons. averaging data transformation An averaging data transformation is a data transformation that has objective averaging. - James Malone + James Malone PERSON: James Malone averaging data transformation @@ -84624,7 +95207,7 @@ to create a common base for comparisons. partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. - James Malone + James Malone PERSON: James Malone partitioning data transformation @@ -84639,9 +95222,9 @@ to create a common base for comparisons. A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi partitioning objective @@ -84654,9 +95237,9 @@ to create a common base for comparisons. background correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi background correction objective @@ -84669,9 +95252,9 @@ to create a common base for comparisons. curve fitting objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi curve fitting objective @@ -84698,9 +95281,9 @@ to create a common base for comparisons. class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. - James Malone - clustering data transformation - unsupervised classification data transformation + James Malone + clustering data transformation + unsupervised classification data transformation PERSON: James Malone class discovery data transformation @@ -84717,12 +95300,12 @@ to create a common base for comparisons. - Fisher's exact test + Fisher's exact test - Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. - James Malone - WEB:http://mathworld.wolfram.com/FishersExactTest.html - Fisher's exact test + Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. + James Malone + WEB:http://mathworld.wolfram.com/FishersExactTest.html + Fisher's exact test @@ -84736,7 +95319,7 @@ to create a common base for comparisons. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone - PERSON: James Malone + PERSON: James Malone center calculation objective @@ -84750,11 +95333,11 @@ to create a common base for comparisons. A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone - clustering objective + clustering objective discriminant analysis objective unsupervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone class discovery objective @@ -84769,10 +95352,10 @@ to create a common base for comparisons. A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone - classification objective + classification objective supervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone class prediction objective @@ -84783,12 +95366,12 @@ class labels for these objects. The resulting predictor can be used to attach cl spread calculation objective - Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean + Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean - is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set + is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set Awaiting English definition from Monnie McGee James Malone - Person:Helen Parkinson + Person:Helen Parkinson spread calculation objective @@ -84815,7 +95398,7 @@ class labels for these objects. The resulting predictor can be used to attach cl center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. - James Malone + James Malone PERSON: James Malone center calculation data transformation @@ -84855,12 +95438,12 @@ class labels for these objects. The resulting predictor can be used to attach cl scaling objective - Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 + Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 - is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum + is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone - Person:Helen Parkinson + Person:Helen Parkinson scaling objective @@ -84919,11 +95502,11 @@ class labels for these objects. The resulting predictor can be used to attach cl error correction objective - Application of a multiple testing correction method + Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson - PERSON: James Malone + PERSON: James Malone error correction objective @@ -84943,7 +95526,7 @@ class labels for these objects. The resulting predictor can be used to attach cl A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. James Malone - EDITOR + EDITOR sequence analysis data transformation @@ -84958,7 +95541,7 @@ class labels for these objects. The resulting predictor can be used to attach cl A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective - WEB: http://en.wikipedia.org/wiki/Cross_validation + WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective @@ -84968,13 +95551,13 @@ class labels for these objects. The resulting predictor can be used to attach cl - merging objective + merging objective merging of columns from two different data sets A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. James Malone combining objective - PERSON: Data Transformation Branch + PERSON: Data Transformation Branch merging objective @@ -85006,11 +95589,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - clustered data visualization + clustered data visualization - A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - clustered data visualization + A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + clustered data visualization @@ -85031,11 +95614,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - gene list visualization + gene list visualization - Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. - James Malone - gene list visualization + Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. + James Malone + gene list visualization @@ -85063,11 +95646,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - classified data visualization + classified data visualization - A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - classified data visualization + A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + classified data visualization @@ -85095,12 +95678,12 @@ class labels for these objects. The resulting predictor can be used to attach cl - background corrected data visualization + background corrected data visualization - A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - Monnie McGee - background corrected data visualization + A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + Monnie McGee + background corrected data visualization @@ -85115,12 +95698,12 @@ class labels for these objects. The resulting predictor can be used to attach cl - survival analysis data transformation + survival analysis data transformation - A data transformation which has the objective of performing survival analysis. - James Malone - PERSON: James Malone - survival analysis data transformation + A data transformation which has the objective of performing survival analysis. + James Malone + PERSON: James Malone + survival analysis data transformation @@ -85135,15 +95718,15 @@ class labels for these objects. The resulting predictor can be used to attach cl - proportional hazards model estimation + proportional hazards model estimation - Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. - PERSON: James Malone - PERSON: Tina Boussard - Cox model - Cox proportional hazards model - WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model - proportional hazards model estimation + Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. + PERSON: James Malone + PERSON: Tina Boussard + Cox model + Cox proportional hazards model + WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model + proportional hazards model estimation @@ -85152,11 +95735,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - correlation study objective + correlation study objective - A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. - PERSON: Tina Boussard - correlation study objective + A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. + PERSON: Tina Boussard + correlation study objective @@ -85165,13 +95748,13 @@ class labels for these objects. The resulting predictor can be used to attach cl - spectrum analysis objective - Calculation of characteristic path length in mass spectrometry + spectrum analysis objective + Calculation of characteristic path length in mass spectrometry - is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. - PERSON: Tina Boussard - Person:Helen Parkinson - spectrum analysis objective + is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. + PERSON: Tina Boussard + Person:Helen Parkinson + spectrum analysis objective @@ -85186,14 +95769,14 @@ class labels for these objects. The resulting predictor can be used to attach cl - tandem mass spectrometry - A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. + tandem mass spectrometry + A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. - Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). - PERSON: James Malone - PERSON: Tina Boussard - PERSON: Tina Boussard - tandem mass spectrometry + Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). + PERSON: James Malone + PERSON: Tina Boussard + PERSON: Tina Boussard + tandem mass spectrometry @@ -85208,15 +95791,15 @@ class labels for these objects. The resulting predictor can be used to attach cl - gas chromatography mass spectrometry + gas chromatography mass spectrometry - Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and + Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. - PERSON: James Malone - PERSON: Tina Boussard - PERSON: Tina Boussard - gas chromatography mass spectrometry + PERSON: James Malone + PERSON: Tina Boussard + PERSON: Tina Boussard + gas chromatography mass spectrometry @@ -85231,12 +95814,12 @@ determinations of compounds. - chi square test + chi square test - The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. - PERSON: James Malone - PERSON: Tina Boussard - chi square test + The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. + PERSON: James Malone + PERSON: Tina Boussard + chi square test @@ -85245,11 +95828,11 @@ determinations of compounds. - ANOVA + ANOVA - ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal. - James Malone - ANOVA + ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal. + James Malone + ANOVA @@ -85258,14 +95841,14 @@ determinations of compounds. - sequential design - PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. + sequential design + PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. - Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does - Philippe Rocca-Serra - MUSC - Provenance: OCI - sequential design + Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does + Philippe Rocca-Serra + MUSC + Provenance: OCI + sequential design @@ -85274,13 +95857,13 @@ determinations of compounds. - observation design - PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. + observation design + PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. - observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. - Philippe Rocca-Serra - OBI branch derived - observation design + observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. + Philippe Rocca-Serra + OBI branch derived + observation design @@ -85290,14 +95873,14 @@ determinations of compounds. obsolete_collection (of entities of organismal origin) - PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] - - a collection is a bfo:aggregate object, that is a set of material object of the same kind - PERSON: Susanna Sansone - ensemble - group - set - PERSON: Philippe Rocca-Serra + PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] + + a collection is a bfo:aggregate object, that is a set of material object of the same kind + PERSON: Susanna Sansone + ensemble + group + set + PERSON: Philippe Rocca-Serra obsolete_collection (of entities of organismal origin) true @@ -85334,8 +95917,8 @@ determinations of compounds. A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish - PERSON: Jennifer Fostel - GROUP: CEBS + PERSON: Jennifer Fostel + GROUP: CEBS pool of specimens @@ -85383,10 +95966,10 @@ determinations of compounds. PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution. A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute. - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra liquid chemical solution - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch chemical solution @@ -85396,14 +95979,14 @@ determinations of compounds. - buffer role - A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution + buffer role + A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution - a role which inheres in some molecular entity realized during the process of buffering - Person:Helen Parkinson - Person:Philippe Rocca-Serra - buffer - OBI + a role which inheres in some molecular entity realized during the process of buffering + Person:Helen Parkinson + Person:Philippe Rocca-Serra + buffer + OBI buffer role @@ -85425,12 +96008,12 @@ determinations of compounds. - solvent role + solvent role PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation - Philippe Rocca-Serra - adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) + Philippe Rocca-Serra + adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role @@ -85452,12 +96035,12 @@ determinations of compounds. - solute role + solute role PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure. solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution - Philippe Rocca-Serra - adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) + Philippe Rocca-Serra + adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) solute role @@ -85584,13 +96167,13 @@ determinations of compounds. comet assay - PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. + PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis - Philippe Rocca-Serra - SCGE assay - single cell gel electrophoresis assay - PMID:7686265 + An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis + Philippe Rocca-Serra + SCGE assay + single cell gel electrophoresis assay + PMID:7686265 comet assay @@ -85633,12 +96216,12 @@ determinations of compounds. PCR-SSCP assay - PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? + PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? - An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions - Philippe Rocca-Serra - polymerase chain reaction-single strand conformation polymorphism assay - PMID:18219595 + An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions + Philippe Rocca-Serra + polymerase chain reaction-single strand conformation polymorphism assay + PMID:18219595 PCR-SSCP assay @@ -85649,11 +96232,11 @@ determinations of compounds. obsolete_liver - PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. + PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. - liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch + liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch obsolete_liver true @@ -85666,11 +96249,11 @@ determinations of compounds. obsolete_adipose tissue - PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. + PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. - adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial derived + adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial derived obsolete_adipose tissue true @@ -85694,11 +96277,11 @@ determinations of compounds. - denatured polymer + denatured polymer Is a polymer which has lost secondary or tertiary structure - PERSON: Alan Ruttenberg - http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 + PERSON: Alan Ruttenberg + http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denatured polymer @@ -85719,12 +96302,12 @@ determinations of compounds. - decapitated organism + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 decapitated organism is an organism which has had it's head removed - Philippe Rocca-Serra + Philippe Rocca-Serra OBI Biomaterial decapitated organism @@ -85741,12 +96324,12 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - validated information - PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." + validated information + PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means. - Person:Philippe Rocca-Serra - OBI + Person:Philippe Rocca-Serra + OBI validated information @@ -85762,15 +96345,15 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - curated information - PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. + curated information + PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. - A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. - 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. - 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference - Person:Bjoern Peters - Person:Philippe Rocca-Serra - OBI + A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. + 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. + 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference + Person:Bjoern Peters + Person:Philippe Rocca-Serra + OBI curated information @@ -85786,12 +96369,12 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - randomized group participant role - A person enrolled in a randomized clinical trial bears a randomized group participant role + randomized group participant role + A person enrolled in a randomized clinical trial bears a randomized group participant role - a role that borne by an organism and realized by some group randomization process - Person:Helen Parkinson - Philippe Rocca-Serra + a role that borne by an organism and realized by some group randomization process + Person:Helen Parkinson + Philippe Rocca-Serra randomized group participant role @@ -85813,12 +96396,12 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer + methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 A methylated polymer which has artificially acquired one or more methyl groups - Philippe Rocca-Serra + Philippe Rocca-Serra OBI Biomaterial methylated polymer @@ -85841,12 +96424,12 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - genetically modified organism + genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 an organism that is the output of a genetic transformation process - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra OBI Biomaterial genetically modified organism @@ -85863,11 +96446,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - predicted data item + predicted data item A data item that was generated on the basis of a calculation or logical reasoning - BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. - Philippe Rocca-Serra; Bjoern Peters + BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. + Philippe Rocca-Serra; Bjoern Peters predicted data item @@ -85883,11 +96466,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - mean-centered data + mean-centered data - a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value - Person:Helen Parkinson - Person:Philippe Rocca-Serra + a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value + Person:Helen Parkinson + Person:Philippe Rocca-Serra mean-centered data @@ -85903,12 +96486,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - edited document - The OBI manuscript is (much) edited imformation + edited document + The OBI manuscript is (much) edited imformation - A document which is the output of a document editing process - Person:Bjoern Peters - Philippe Rocca-Serra + A document which is the output of a document editing process + Person:Bjoern Peters + Philippe Rocca-Serra edited document @@ -85935,12 +96518,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - dissolved material entity - Salt molecules that have been mixed into water + dissolved material entity + Salt molecules that have been mixed into water - A material entity that has been going through a process of being put into solution - Person:Bjoern Peters - Philippe Rocca-Serra + A material entity that has been going through a process of being put into solution + Person:Bjoern Peters + Philippe Rocca-Serra dissolved material entity @@ -85956,14 +96539,14 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - extraction - nucleic acid extraction using phenol chloroform + extraction + nucleic acid extraction using phenol chloroform - A material separation in which a desired component of an input material is separated from the remainder + A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. - Person:Bjoern Peters - Philippe Rocca-Serra + Person:Bjoern Peters + Philippe Rocca-Serra extraction @@ -85985,12 +96568,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - filtration + filtration PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device - Philippe Rocca-Serra - OBI-Branch: adapted from wikipedia and wordnet + Philippe Rocca-Serra + OBI-Branch: adapted from wikipedia and wordnet filtration @@ -86012,12 +96595,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - centrifugation + centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation - Philippe Rocca-Serra - adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm + Philippe Rocca-Serra + adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation @@ -86033,12 +96616,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - staining + staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. - Philippe Rocca-Serra - adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining + Philippe Rocca-Serra + adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining @@ -86066,12 +96649,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - washing + washing PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch washing @@ -86099,12 +96682,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - irradiation + irradiation PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves - Philippe Rocca-Serra - adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) + Philippe Rocca-Serra + adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) irradiation @@ -86132,13 +96715,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - polymerization + polymerization PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3. polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight PRS:22102008: need to import catalyst from CHEBI 35223 - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch polymerization @@ -86148,12 +96731,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - trypsination + trypsination The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483 trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity - Philippe Rocca-Serra - OBI PA + Philippe Rocca-Serra + OBI PA trypsination @@ -86185,12 +96768,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - enzymatic ligation + enzymatic ligation PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch enzymatic ligation @@ -86212,12 +96795,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - storage + storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch storage @@ -86240,13 +96823,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - cell lysis + cell lysis PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41. cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. - BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. - Philippe Rocca-Serra - adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] + BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. + Philippe Rocca-Serra + adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] cell lysis @@ -86262,12 +96845,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - electrocution + electrocution PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376. electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. - Philippe Rocca-Serra - OBI branch + Philippe Rocca-Serra + OBI branch electrocution @@ -86277,13 +96860,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - cervical dislocation + cervical dislocation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3 cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax) - Philippe Rocca-Serra - OBI branch + Philippe Rocca-Serra + OBI branch cervical dislocation @@ -86293,12 +96876,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - asphyxiation + asphyxiation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms. - Philippe Rocca-Serra - OBI branch + Philippe Rocca-Serra + OBI branch asphyxiation @@ -86314,14 +96897,14 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - intentional overdosing + intentional overdosing In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097 intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death - Philippe Rocca-Serra + Philippe Rocca-Serra lethal injection - OBI Biomaterial + OBI Biomaterial intentional overdosing @@ -86331,12 +96914,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - decapitation + decapitation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..) - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch decapitation @@ -86346,12 +96929,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - group randomization + group randomization PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. - Philippe Rocca-Serra - adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] + Philippe Rocca-Serra + adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] group randomization @@ -86362,11 +96945,11 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 obsolete_activation - PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. + PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. - a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) - Philippe Rocca-Serra - OBI-Branch + a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) + Philippe Rocca-Serra + OBI-Branch obsolete_activation true @@ -86384,12 +96967,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - immobilization + immobilization PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch immobilization @@ -86415,13 +96998,13 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - nucleic acid hybridization + nucleic acid hybridization PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. - Philippe Rocca-Serra - adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] - hybridization assay + Philippe Rocca-Serra + adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] + hybridization assay nucleic acid hybridization @@ -86465,12 +97048,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - elution + elution PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13. the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions) - Philippe Rocca-Serra - wordnet.princeton.edu/perl/webwn + Philippe Rocca-Serra + wordnet.princeton.edu/perl/webwn elution @@ -86490,8 +97073,8 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81 a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch DNA Subtraction @@ -86513,13 +97096,13 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - document editing + document editing Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292 is a planned process with specified input original document and specified output edited document - Philippe Rocca-Serra and OBI consortium - adapted from wikipedia + Philippe Rocca-Serra and OBI consortium + adapted from wikipedia document editing @@ -86541,12 +97124,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - prediction + prediction Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190 a process by which an event or an entity is described before it actually happens or is being discovered and identified. - Philippe Rocca-Serra - OBI + Philippe Rocca-Serra + OBI prediction @@ -86556,12 +97139,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - validation + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results - Philippe Rocca-Serra - adapted from wordnet (wkipedia) + Philippe Rocca-Serra + adapted from wordnet (wkipedia) validation @@ -86583,13 +97166,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - electroporation + electroporation PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13. a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA - Philippe Rocca-Serra - electropermeabilization - WEB:http://en.wikipedia.org/wiki/Electroporation + Philippe Rocca-Serra + electropermeabilization + WEB:http://en.wikipedia.org/wiki/Electroporation electroporation @@ -86599,12 +97182,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - digital curation + digital curation PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. - Philippe Rocca-Serra - wikipedia + Philippe Rocca-Serra + wikipedia digital curation @@ -86614,12 +97197,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - A10-Analyzer + A10-Analyzer - A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. - John Quinn - http://www.apogeeflow.com/flow_cytometry_products.htm - A10-Analyzer + A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. + John Quinn + http://www.apogeeflow.com/flow_cytometry_products.htm + A10-Analyzer @@ -86628,12 +97211,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - A40-MiniFCM + A40-MiniFCM - A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. - John Quinn - http://www.apogeeflow.com/flow_cytometry_products.htm - A40-MiniFCM + A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. + John Quinn + http://www.apogeeflow.com/flow_cytometry_products.htm + A40-MiniFCM @@ -86648,16 +97231,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - analog-to-digital converter - The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. + analog-to-digital converter + The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. - An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. - John Quinn - Melanie Courtot - A-D - A2D - http://en.wiktionary.org/wiki/Analog-to-Digital_Converter - analog-to-digital converter + An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. + John Quinn + Melanie Courtot + A-D + A2D + http://en.wiktionary.org/wiki/Analog-to-Digital_Converter + analog-to-digital converter @@ -86696,13 +97279,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cytometer analyzer - FACS Calibur, Luminex 100 + flow cytometer analyzer + FACS Calibur, Luminex 100 - An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cytometer analyzer + An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cytometer analyzer @@ -86711,13 +97294,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - arc lamp - The Jablochkoff Candle + arc lamp + The Jablochkoff Candle - Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point. - John Quinn - http://en.wikipedia.org/wiki/Arc_lamp - arc lamp + Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point. + John Quinn + http://en.wikipedia.org/wiki/Arc_lamp + arc lamp @@ -86726,14 +97309,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - argon ion laser - argon ion laser in a cytometer + argon ion laser + argon ion laser in a cytometer - An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Laser#Gas_lasers - argon ion laser + An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Laser#Gas_lasers + argon ion laser @@ -86742,13 +97325,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - avalanche photodiode - C30644E - InGaAs Avalanche Photodiode + avalanche photodiode + C30644E - InGaAs Avalanche Photodiode - An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - avalanche photodiode + An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + avalanche photodiode @@ -86757,12 +97340,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Bactiflow + Bactiflow - A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes. - John Quinn - http://www.chemunex.com/products/chemframe.htm - Bactiflow + A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes. + John Quinn + http://www.chemunex.com/products/chemframe.htm + Bactiflow @@ -86771,13 +97354,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - band pass filter - 530/30 BP filter, 585/42 BP filter + band pass filter + 530/30 BP filter, 585/42 BP filter - A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. - Person:John Quinn - http://en.wikipedia.org/wiki/Band_pass_filter - band pass filter + A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. + Person:John Quinn + http://en.wikipedia.org/wiki/Band_pass_filter + band pass filter @@ -86786,13 +97369,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter1000 - BioSorter 1000 at TSRI Flow Cytometry Core Facility + BioSorter1000 + BioSorter 1000 at TSRI Flow Cytometry Core Facility - A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter1000 + A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter1000 @@ -86801,13 +97384,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter2000 - BioSorter 2000 at TSRI Flow Cytometry Core Facility + BioSorter2000 + BioSorter 2000 at TSRI Flow Cytometry Core Facility - A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter2000 + A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter2000 @@ -86816,13 +97399,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter250 - BioSorter 250 at TSRI Flow Cytometry Core Facility + BioSorter250 + BioSorter 250 at TSRI Flow Cytometry Core Facility - A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter250 + A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter250 @@ -86831,13 +97414,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter500 - BioSorter 500 at TSRI Flow Cytometry Core Facility + BioSorter500 + BioSorter 500 at TSRI Flow Cytometry Core Facility - A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter500 + A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter500 @@ -86846,12 +97429,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Cell Lab Quanta SC + Cell Lab Quanta SC - A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells. - John Quinn - http://www.beckmancoulter.com/cell-lab - Cell Lab Quanta SC + A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells. + John Quinn + http://www.beckmancoulter.com/cell-lab + Cell Lab Quanta SC @@ -86872,13 +97455,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - charge plate - LSR2 charge plate + charge plate + LSR2 charge plate - Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - charge plate + Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + charge plate @@ -86887,13 +97470,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - cell sorter collection tube - LSR2 collection tube + cell sorter collection tube + LSR2 collection tube - Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - cell sorter collection tube + Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + cell sorter collection tube @@ -86902,12 +97485,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Cyan + Cyan - A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells. - John Quinn - http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm - Cyan + A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells. + John Quinn + http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm + Cyan @@ -86916,12 +97499,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CYFlow ML + CYFlow ML - A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting. - John Quinn - http://www.partec.de/products/cyflow-ml.html - CYFlow ML + A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting. + John Quinn + http://www.partec.de/products/cyflow-ml.html + CYFlow ML @@ -86930,12 +97513,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CyFlow SL + CyFlow SL - a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. - John Quinn - http://www.partec.de/products/cyflow.html - CyFlow SL + a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. + John Quinn + http://www.partec.de/products/cyflow.html + CyFlow SL @@ -86944,12 +97527,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CyFlow SL3 + CyFlow SL3 - A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement. - John Quinn - http://www.partec.de/products/cyflowsl3.html - CyFlow SL3 + A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement. + John Quinn + http://www.partec.de/products/cyflowsl3.html + CyFlow SL3 @@ -86958,13 +97541,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - CyFlow Space - CyFlow Space at TSRI Flow Cytometry Core Facility + CyFlow Space + CyFlow Space at TSRI Flow Cytometry Core Facility - A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. - John Quinn - http://www.partec.de/products/cyflowspace.html - CyFlow Space + A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. + John Quinn + http://www.partec.de/products/cyflowspace.html + CyFlow Space @@ -86979,13 +97562,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - CytoBuoy - CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations + CytoBuoy + CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations - A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. - John Quinn, Melanie Courtot - http://www.cytobuoy.com/ - CytoBuoy flow cytometer analyzer + A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. + John Quinn, Melanie Courtot + http://www.cytobuoy.com/ + CytoBuoy flow cytometer analyzer @@ -86994,12 +97577,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CytoSence + CytoSence - A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. - John Quinn - http://www.cytobuoy.com/ - CytoSence + A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. + John Quinn + http://www.cytobuoy.com/ + CytoSence @@ -87008,12 +97591,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CytoSub + CytoSub - A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle. - John Quinn - http://www.cytobuoy.com/ - CytoSub + A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle. + John Quinn + http://www.cytobuoy.com/ + CytoSub @@ -87022,13 +97605,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - dichroic filter - Cy3 Dichroic Filter + dichroic filter + Cy3 Dichroic Filter - A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. - John Quinn - http://en.wikipedia.org/wiki/Dichroic_filter - dichroic filter + A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. + John Quinn + http://en.wikipedia.org/wiki/Dichroic_filter + dichroic filter @@ -87037,13 +97620,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - dichroic mirror - ViewLux Alexa 594 dichroic mirror + dichroic mirror + ViewLux Alexa 594 dichroic mirror - A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. - John Quinn - http://en.wikipedia.org/wiki/Dichroic_mirror - dichroic mirror + A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. + John Quinn + http://en.wikipedia.org/wiki/Dichroic_mirror + dichroic mirror @@ -87058,13 +97641,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - differential pressure gauge - LSR2 differential pressure gauge + differential pressure gauge + LSR2 differential pressure gauge - Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - differential pressure gauge + Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + differential pressure gauge @@ -87073,13 +97656,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - diode laser - FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. + diode laser + FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. - A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. - Daniel Schober - John Quinn - diode laser + A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. + Daniel Schober + John Quinn + diode laser @@ -87088,14 +97671,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - dye laser - Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. + dye laser + Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. - A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. - Daniel Schober - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - dye laser + A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. + Daniel Schober + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + dye laser @@ -87104,13 +97687,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Calibur - FACS Calibur at TFL, BCCRC, Vancouver + FACS Calibur + FACS Calibur at TFL, BCCRC, Vancouver - The FACS Calibur is one of the most popular cytometers in use for research. - John Quinn - http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11 - FACS Calibur + The FACS Calibur is one of the most popular cytometers in use for research. + John Quinn + http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11 + FACS Calibur @@ -87119,12 +97702,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Canto + FACS Canto - A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications. - John Quinn - http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf - FACS Canto + A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications. + John Quinn + http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf + FACS Canto @@ -87133,12 +97716,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Canto2 + FACS Canto2 - A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications. - John Quinn - http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01 - FACS Canto2 + A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications. + John Quinn + http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01 + FACS Canto2 @@ -87147,12 +97730,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Scan + FACS Scan - A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. - John Quinn - http://www.brc.ubc.ca/brc/facs.html - FACS Scan + A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. + John Quinn + http://www.brc.ubc.ca/brc/facs.html + FACS Scan @@ -87161,13 +97744,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACSAria - FACSAria at TSRI Flow Cytometry Core Facility + FACSAria + FACSAria at TSRI Flow Cytometry Core Facility - A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. - John Quinn - http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf - FACSAria + A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. + John Quinn + http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf + FACSAria @@ -87176,13 +97759,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACSvantage - FACSvantage at TSRI Flow Cytometry Core Facility + FACSvantage + FACSvantage at TSRI Flow Cytometry Core Facility - The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. - John Quinn - http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 - FACSvantage + The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. + John Quinn + http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 + FACSvantage @@ -87191,12 +97774,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FC 500 + FC 500 - A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. - John Quinn - http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp - FC 500 + A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. + John Quinn + http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp + FC 500 @@ -87211,14 +97794,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cell - Biofilm Flow Cell + flow cell + Biofilm Flow Cell - Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. - Person:John Quinn - flow_cell - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cell + Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. + Person:John Quinn + flow_cell + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cell @@ -87263,13 +97846,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cytometer - FACS Calibur + flow cytometer + FACS Calibur - A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. - John Quinn - http://en.wikipedia.org/wiki/Flow_cytometer - flow cytometer + A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. + John Quinn + http://en.wikipedia.org/wiki/Flow_cytometer + flow cytometer @@ -87291,13 +97874,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - fluid pressure regulator - LSR2 fluid pressure regulator + fluid pressure regulator + LSR2 fluid pressure regulator - Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. - Person: John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - fluid pressure regulator + Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. + Person: John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + fluid pressure regulator @@ -87306,14 +97889,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - gas laser - helium-neon gas laser used to erradiate cells in a flow cytometer. + gas laser + helium-neon gas laser used to erradiate cells in a flow cytometer. - A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Gas_laser - gas laser + A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Gas_laser + gas laser @@ -87322,12 +97905,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava EasyCyte Mini + Guava EasyCyte Mini - A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - http://www.guavatechnologies.com/main/products/easyCyteMini.cfm - Guava EasyCyte Mini + A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + http://www.guavatechnologies.com/main/products/easyCyteMini.cfm + Guava EasyCyte Mini @@ -87336,12 +97919,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava EasyCyte Plus + Guava EasyCyte Plus - A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - http://www.guavatechnologies.com/main/products/easycyte-new.cfm - Guava EasyCyte Plus + A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + http://www.guavatechnologies.com/main/products/easycyte-new.cfm + Guava EasyCyte Plus @@ -87350,13 +97933,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava Personal Cell Analysis + Guava Personal Cell Analysis - A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - Guava_PCA - http://www.guavatechnologies.com/main/products/PCA-new.cfm - Guava Personal Cell Analysis + A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + Guava_PCA + http://www.guavatechnologies.com/main/products/PCA-new.cfm + Guava Personal Cell Analysis @@ -87365,13 +97948,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava Personal Cell Analysis-96 + Guava Personal Cell Analysis-96 - The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - Guava_PCA-96 - http://www.guavatechnologies.com/main/products/PCA-96new.cfm - Guava Personal Cell Analysis-96 + The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + Guava_PCA-96 + http://www.guavatechnologies.com/main/products/PCA-96new.cfm + Guava Personal Cell Analysis-96 @@ -87380,13 +97963,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - helium cadmium ion laser - KIMMON HeCd 325nm laser + helium cadmium ion laser + KIMMON HeCd 325nm laser - A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer. - John Quinn - http://en.wikipedia.org/wiki/Laser#Gas_lasers - helium cadmium ion laser + A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer. + John Quinn + http://en.wikipedia.org/wiki/Laser#Gas_lasers + helium cadmium ion laser @@ -87395,14 +97978,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - helium neon ion laser - A helium neon laser can by used to irradiate cells in a flow cytometer. + helium neon ion laser + A helium neon laser can by used to irradiate cells in a flow cytometer. - A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Laser#Gas_lasers - helium neon ion laser + A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Laser#Gas_lasers + helium neon ion laser @@ -87423,14 +98006,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - Amnis ImageStream + Amnis ImageStream - The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer. - It has both components, an Image cytometer and a flow cytometer. - John Quinn - Melanie Courtot - http://www.amnis.com/ - Amnis ImageStream + The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer. + It has both components, an Image cytometer and a flow cytometer. + John Quinn + Melanie Courtot + http://www.amnis.com/ + Amnis ImageStream @@ -87439,12 +98022,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - inFlux Analyzer + inFlux Analyzer - The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. - John Quinn - http://www.cytopeia.com/analyzer.htm - inFlux Analyzer + The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. + John Quinn + http://www.cytopeia.com/analyzer.htm + inFlux Analyzer @@ -87453,13 +98036,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Influx Cell Sorter - Influx Cell Sorter at TSRI Flow Cytometry Core Facility + Influx Cell Sorter + Influx Cell Sorter at TSRI Flow Cytometry Core Facility - A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. - John Quinn - http://www.cytopeia.com/sorter.htm - Influx Cell Sorter + A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. + John Quinn + http://www.cytopeia.com/sorter.htm + Influx Cell Sorter @@ -87483,14 +98066,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - ion laser - 2 Watt Lexel 88 Argon Ion laser + ion laser + 2 Watt Lexel 88 Argon Ion laser - An ion laser is a gas laser which uses an ionized gas as its lasing medium. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Ion_laser - ion laser + An ion laser is a gas laser which uses an ionized gas as its lasing medium. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Ion_laser + ion laser @@ -87514,13 +98097,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - krypton ion laser - Lexel 95L krypton laser + krypton ion laser + Lexel 95L krypton laser - A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however. - Daniel Schober - John Quinn - krypton ion laser + A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however. + Daniel Schober + John Quinn + krypton ion laser @@ -87529,14 +98112,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - LactoScope C4 - LactoScope C4 Automatic Economical + LactoScope C4 + LactoScope C4 Automatic Economical - A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy. - Josef Spidlen - Melanie Courtot - http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm - LactoScope C4 + A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy. + Josef Spidlen + Melanie Courtot + http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm + LactoScope C4 @@ -87545,15 +98128,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - laser - A laser is the most common way to irradiate a cell in a flow cytometer. + laser + A laser is the most common way to irradiate a cell in a flow cytometer. - A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. - Daniel Schober - light amplification by the stimulated emission of radiation - John Quinn - http://en.wikipedia.org/wiki/Laser - laser + A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. + Daniel Schober + light amplification by the stimulated emission of radiation + John Quinn + http://en.wikipedia.org/wiki/Laser + laser @@ -87568,14 +98151,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - light source + light source - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. - Elizabeth M. Goralczyk - John Quinn - Olga Tchuvatkina - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - light source + A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. + Elizabeth M. Goralczyk + John Quinn + Olga Tchuvatkina + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + light source @@ -87584,13 +98167,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - logarithmic voltage amplifier - HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH + logarithmic voltage amplifier + HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH - A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - logarithmic voltage amplifier + A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + logarithmic voltage amplifier @@ -87599,13 +98182,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - long pass filter - 750 LP filter + long pass filter + 750 LP filter - A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. - John Quinn - http://en.wikipedia.org/wiki/high-pass_filter - long pass filter + A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. + John Quinn + http://en.wikipedia.org/wiki/high-pass_filter + long pass filter @@ -87614,13 +98197,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - LSR2 - LSR2 at TSRI Flow Cytometry Core Facility + LSR2 + LSR2 at TSRI Flow Cytometry Core Facility - A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. - John Quinn - http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf - LSR2 + A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. + John Quinn + http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf + LSR2 @@ -87629,12 +98212,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Luminex 100 + Luminex 100 - The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette. - John Quinn - http://www.luminexcorp.com/products/luminex_100IS.html - Luminex 100 + The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette. + John Quinn + http://www.luminexcorp.com/products/luminex_100IS.html + Luminex 100 @@ -87643,12 +98226,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Luminex 200 + Luminex 200 - A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation - John Quinn - http://www.luminexcorp.com/support/faqs.html - Luminex 200 + A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation + John Quinn + http://www.luminexcorp.com/support/faqs.html + Luminex 200 @@ -87657,12 +98240,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - MACS Quant + MACS Quant - A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. - John Quinn - http://www.miltenyi.com - MACS Quant + A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. + John Quinn + http://www.miltenyi.com + MACS Quant @@ -87671,13 +98254,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - metal vapor laser - Gold vapor laser, Helium-cadmium metal-vapor laser + metal vapor laser + Gold vapor laser, Helium-cadmium metal-vapor laser - A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - metal vapor laser + A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + metal vapor laser @@ -87686,13 +98269,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - mixed argon-krypton gas laser - argon-krypton laser in a cytometer + mixed argon-krypton gas laser + argon-krypton laser in a cytometer - A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. - John Quinn - http://www.eio.com/repairfaq/sam/laserarg.htm - mixed argon-krypton gas laser + A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. + John Quinn + http://www.eio.com/repairfaq/sam/laserarg.htm + mixed argon-krypton gas laser @@ -87701,13 +98284,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - MoFlo - MoFlo at TSRI Flow Cytometry Core Facility + MoFlo + MoFlo at TSRI Flow Cytometry Core Facility - A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium. - John Quinn - http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 - MoFlo + A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium. + John Quinn + http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 + MoFlo @@ -87732,13 +98315,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - neodymium-YAG laser - Neodymium-YAG Laser in DURIP99 System + neodymium-YAG laser + Neodymium-YAG Laser in DURIP99 System - A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer. - Daniel Schober - John Quinn - neodymium-YAG laser + A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer. + Daniel Schober + John Quinn + neodymium-YAG laser @@ -87753,14 +98336,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - obscuration bar - obscuration bar in a flow cytometer + obscuration bar + obscuration bar in a flow cytometer - An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. - Daniel Schober - Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 - John Quinn - obscuration bar + An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. + Daniel Schober + Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 + John Quinn + obscuration bar @@ -87775,13 +98358,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - optical filter - 720 LP filter, 580/30 BP filter + optical filter + 720 LP filter, 580/30 BP filter - An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. - John Quinn - http://en.wikipedia.org/wiki/Optical_filter - optical filter + An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. + John Quinn + http://en.wikipedia.org/wiki/Optical_filter + optical filter @@ -87808,14 +98391,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - optical subsystem - optical subsystem of a cytometer + optical subsystem + optical subsystem of a cytometer - A device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles. - DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one. - Person: Daniel Schober - John Quinn - optical subsystem + A device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles. + DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one. + Person: Daniel Schober + John Quinn + optical subsystem @@ -87846,13 +98429,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - photodetector - A photomultiplier tube, a photo diode + photodetector + A photomultiplier tube, a photo diode - A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. - John Quinn - http://einstein.stanford.edu/content/glossary/glossary.html - photodetector + A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. + John Quinn + http://einstein.stanford.edu/content/glossary/glossary.html + photodetector @@ -87861,13 +98444,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - photodiode - Avalanche photodiode + photodiode + Avalanche photodiode - A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. - John Quinn - http://cyto.mednet.ucla.edu/Protocols/flow.htm - photodiode + A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. + John Quinn + http://cyto.mednet.ucla.edu/Protocols/flow.htm + photodiode @@ -87895,13 +98478,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - photomultiplier tube - R9647 by manufactured by Hamamatsu + photomultiplier tube + R9647 by manufactured by Hamamatsu - A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. - John Quinn - http://cyto.mednet.ucla.edu/Protocols/flow.htm - photomultiplier tube + A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. + John Quinn + http://cyto.mednet.ucla.edu/Protocols/flow.htm + photomultiplier tube @@ -87916,13 +98499,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - piezo electric crystal + piezo electric crystal quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - think this is natural thing, not a device HP/JF + think this is natural thing, not a device HP/JF piezo electric crystal @@ -87938,14 +98521,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - plate loader - FC 500 plate loader + plate loader + FC 500 plate loader - Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications. - measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future. - John Quinn - http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf - plate loader + Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications. + measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future. + John Quinn + http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf + plate loader @@ -87954,13 +98537,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - preamplifier - Built in preamplifier in a Hamamatsu H9656 PMT + preamplifier + Built in preamplifier in a Hamamatsu H9656 PMT - A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - preamplifier + A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + preamplifier @@ -87969,13 +98552,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - quartz cuvette flow chamber - CVF-Q-10 flow chamber, CV-Q-10 flow chamber + quartz cuvette flow chamber + CVF-Q-10 flow chamber, CV-Q-10 flow chamber - A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - quartz cuvette flow chamber + A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + quartz cuvette flow chamber @@ -87984,13 +98567,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Reflection - Reflection at TSRI Flow Cytometry Core Facility + Reflection + Reflection at TSRI Flow Cytometry Core Facility - A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells. - John Quinn - http://www.i-cyt.com/reflection.htm - Reflection + A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells. + John Quinn + http://www.i-cyt.com/reflection.htm + Reflection @@ -87999,13 +98582,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - cytometer sample tube - sample tube in a cytometer + cytometer sample tube + sample tube in a cytometer - A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - cytometer sample tube + A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + cytometer sample tube @@ -88026,13 +98609,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - sheath tank - LSR2 sheath tank + sheath tank + LSR2 sheath tank - Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - sheath tank + Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + sheath tank @@ -88041,13 +98624,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - short pass filter - 620 SP filter + short pass filter + 620 SP filter - A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. - John Quinn - http://en.wikipedia.org/wiki/Low-pass_filter - short pass filter + A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. + John Quinn + http://en.wikipedia.org/wiki/Low-pass_filter + short pass filter @@ -88056,13 +98639,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - solid state laser - Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command + solid state laser + Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command - A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser. - Daniel Schober - http://en.wikipedia.org/wiki/Solid-state_laser - solid state laser + A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser. + Daniel Schober + http://en.wikipedia.org/wiki/Solid-state_laser + solid state laser @@ -88071,12 +98654,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Somacount + Somacount - A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk. - John Quinn - http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 - Somacount + A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk. + John Quinn + http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 + Somacount @@ -88085,13 +98668,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - SomaScope - SomaScope Mark II Automatic Economical + SomaScope + SomaScope Mark II Automatic Economical - The SomaScope is an instrument to quantify somatic cells in milk. - Josef Spidlen - http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10 - SomaScope + The SomaScope is an instrument to quantify somatic cells in milk. + Josef Spidlen + http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10 + SomaScope @@ -88131,14 +98714,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cytometer sorter - BioSorter2000, LSR2 + flow cytometer sorter + BioSorter2000, LSR2 - A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. - John Quinn - Melanie Courtot - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cytometer sorter + A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. + John Quinn + Melanie Courtot + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cytometer sorter @@ -88159,13 +98742,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - syringe pump - NE-1000 Single Syringe Pump + syringe pump + NE-1000 Single Syringe Pump - Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. - Person:John Quinn - http://www.answers.com/topic/syringe, 2007-05-11 - syringe pump + Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. + Person:John Quinn + http://www.answers.com/topic/syringe, 2007-05-11 + syringe pump @@ -88180,14 +98763,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - voltage amplifier - Linear amplifier, log amplifier, microwave amplifier + voltage amplifier + Linear amplifier, log amplifier, microwave amplifier - A voltage amplifier is a device that amplifies the voltage signal. - Frank Gibson - John Quinn - http://en.wiktionary.org/wiki/amplifier - voltage amplifier + A voltage amplifier is a device that amplifies the voltage signal. + Frank Gibson + John Quinn + http://en.wiktionary.org/wiki/amplifier + voltage amplifier @@ -88202,13 +98785,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - waste tank - LSR2 waste tank + waste tank + LSR2 waste tank - Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. - Person:John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - waste tank + Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. + Person:John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + waste tank @@ -88223,13 +98806,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - DNA sequencer - ABI 377 DNA Sequencer, ABI 310 DNA Sequencer + DNA sequencer + ABI 377 DNA Sequencer, ABI 310 DNA Sequencer - A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. - Trish Whetzel - MO - DNA sequencer + A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. + Trish Whetzel + MO + DNA sequencer @@ -88250,13 +98833,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - array scanner - GenePix 4200A, GenePix4000B + array scanner + GenePix 4200A, GenePix4000B - An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip - Trish Whetzel - GROUP: MGED Ontology - array scanner + An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip + Trish Whetzel + GROUP: MGED Ontology + array scanner @@ -88271,13 +98854,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - arrayer - BioRobotics Microgrid II TAS, Affymetrix GMS 417 + arrayer + BioRobotics Microgrid II TAS, Affymetrix GMS 417 - A device which deposits biological material onto a substrate in a defined pattern. - Trish Whetzel - MO_697 arrayer - arrayer + A device which deposits biological material onto a substrate in a defined pattern. + Trish Whetzel + MO_697 arrayer + arrayer @@ -88320,14 +98903,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - centrifuge + centrifuge - A device with a rapidly rotating container that applies centrifugal force to its contents - Melanie Courtot - Person: Jennifer Fostel - Trish Whetzel - http://en.wikipedia.org/wiki/Centrifuge - centrifuge + A device with a rapidly rotating container that applies centrifugal force to its contents + Melanie Courtot + Person: Jennifer Fostel + Trish Whetzel + http://en.wikipedia.org/wiki/Centrifuge + centrifuge @@ -88342,14 +98925,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - computer - Apple PowerBook, Dell OptiPlex + computer + Apple PowerBook, Dell OptiPlex - A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. - Melanie Courtot - Trish Whetzel - http://en.wikipedia.org/wiki/Computer - computer + A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. + Melanie Courtot + Trish Whetzel + http://en.wikipedia.org/wiki/Computer + computer @@ -88364,13 +98947,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - heating block - An instrument used to heat and/or maintain material at a set temperature. + heating block + An instrument used to heat and/or maintain material at a set temperature. - A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay - Daniel Schober - MO - heating block + A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay + Daniel Schober + MO + heating block @@ -88385,14 +98968,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - homogenizer - mortar, blender + homogenizer + mortar, blender - A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. - Melanie Courtot - Trish Whetzel - http://en.wikipedia.org/wiki/Homogenizer - homogenizer + A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. + Melanie Courtot + Trish Whetzel + http://en.wikipedia.org/wiki/Homogenizer + homogenizer @@ -88413,13 +98996,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - hybridization chamber - Glass Array Hybridization Cassette + hybridization chamber + Glass Array Hybridization Cassette - A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. - Trish Whetzel - MO_563 hybridization_chamber - hybridization chamber + A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. + Trish Whetzel + MO_563 hybridization_chamber + hybridization chamber @@ -88440,13 +99023,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - hybridization station - Labnet Problot12 + hybridization station + Labnet Problot12 - A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. - Trish Whetzel - MO_497 hybridization station - hybridization station + A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. + Trish Whetzel + MO_497 hybridization station + hybridization station @@ -88461,15 +99044,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - liquid handler - Beckman BioMek 2000 + liquid handler + Beckman BioMek 2000 - A device that is used for automated liquid transfer and handling. - liquid_handling_instrument - MO_868 liquid_handler - DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. - DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. - liquid handler + A device that is used for automated liquid transfer and handling. + liquid_handling_instrument + MO_868 liquid_handler + DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. + DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. + liquid handler @@ -88490,13 +99073,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - oligonucleotide synthesizer - Automated Multiplex Oligonucleotide Synthesizer + oligonucleotide synthesizer + Automated Multiplex Oligonucleotide Synthesizer - An instrument used to chemically synthesize oligonucleotides. - Trish Whetzel - MO - oligonucleotide synthesizer + An instrument used to chemically synthesize oligonucleotides. + Trish Whetzel + MO + oligonucleotide synthesizer @@ -88511,13 +99094,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - sonicator - Sonicator 3000 + sonicator + Sonicator 3000 - A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. - Trish Whetzel - MO - sonicator + A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. + Trish Whetzel + MO + sonicator @@ -88532,14 +99115,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - spectrophotometer - Helios Gamma Spectrophotometer + spectrophotometer + Helios Gamma Spectrophotometer - A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. - Melanie Courtot - Trish Whetzel - MO - spectrophotometer + A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. + Melanie Courtot + Trish Whetzel + MO + spectrophotometer @@ -88560,18 +99143,18 @@ Manual editing of automatically recorded data in an anesthesia information manag - thermal cycler - Piko(tm) 96-well Thermal Cycler + thermal cycler + Piko(tm) 96-well Thermal Cycler - An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. - Melanie Courtot - Trish Whetzel - DNA_amplifier - PCR_machine - Polymerase_Chain_Reaction_ machine - thermocycler - MO - thermal cycler + An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. + Melanie Courtot + Trish Whetzel + DNA_amplifier + PCR_machine + Polymerase_Chain_Reaction_ machine + thermocycler + MO + thermal cycler @@ -88598,13 +99181,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - vacuum dryer - Model 777 Microarray Oven + vacuum dryer + Model 777 Microarray Oven - An instrument which removes liquid by the application of negative pressure, i.e. vacuum. - Trish Whetzel - MO - vacuum dryer + An instrument which removes liquid by the application of negative pressure, i.e. vacuum. + Trish Whetzel + MO + vacuum dryer @@ -88619,15 +99202,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - vortexer - VWR Genie 2 + vortexer + VWR Genie 2 - A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. - Melanie Courtot - Trish Whetzel - vortex_mixer - http://en.wikipedia.org/wiki/Vortex_mixer - vortexer + A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. + Melanie Courtot + Trish Whetzel + vortex_mixer + http://en.wikipedia.org/wiki/Vortex_mixer + vortexer @@ -88642,13 +99225,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microarray wash station - ArrayIt(r) Microarray Wash Station + microarray wash station + ArrayIt(r) Microarray Wash Station - A device that is used to wash Affymetrix-type arrays. - Trish Whetzel - MO_626 wash_station - microarray wash station + A device that is used to wash Affymetrix-type arrays. + Trish Whetzel + MO_626 wash_station + microarray wash station @@ -88669,16 +99252,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - temperature control bath - VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. + temperature control bath + VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. - A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. - Alan Ruttenburg - Daniel Schober - Frank Gibson - OBI Instrument branch - DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). - temperature control bath + A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. + Alan Ruttenburg + Daniel Schober + Frank Gibson + OBI Instrument branch + DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). + temperature control bath @@ -88700,15 +99283,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - molecular crosslinker - Stratalinker + molecular crosslinker + Stratalinker - A device that is able to chemically join two or more molecules. - AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. - Trish Whetzel - molecular crosslinker - MO ?? cannot be found in MO - molecular crosslinker + A device that is able to chemically join two or more molecules. + AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. + Trish Whetzel + molecular crosslinker + MO ?? cannot be found in MO + molecular crosslinker @@ -88741,13 +99324,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - image cytometer - The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. + image cytometer + The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. - An image_cytometer is an instrument for image-based study or measurement of cells. - Melanie Courtot - http://web.mit.edu/solab/Research/ImageCytometry.html - image cytometer + An image_cytometer is an instrument for image-based study or measurement of cells. + Melanie Courtot + http://web.mit.edu/solab/Research/ImageCytometry.html + image cytometer @@ -88780,12 +99363,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - cytometer + cytometer - A cytometer is an instrument for counting and/or measuring characteristics of cells. - Melanie Courtot - http://medical.merriam-webster.com/medical/cytometer - cytometer + A cytometer is an instrument for counting and/or measuring characteristics of cells. + Melanie Courtot + http://medical.merriam-webster.com/medical/cytometer + cytometer @@ -88806,16 +99389,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - gel tank - CHEF gel box, slab gel box, capillary electrophoresis + gel tank + CHEF gel box, slab gel box, capillary electrophoresis - A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. - Person:Frank Gibson - Person:Kevin Clancy - electrophoresis box - electrophoresis unit - sep:00095 - gel tank + A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. + Person:Frank Gibson + Person:Kevin Clancy + electrophoresis box + electrophoresis unit + sep:00095 + gel tank @@ -88830,20 +99413,20 @@ Manual editing of automatically recorded data in an anesthesia information manag - power supply - A AC/DC transformer that generates the reqired power for an electrophoresis apparatus + power supply + A AC/DC transformer that generates the reqired power for an electrophoresis apparatus - A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time. - Daniel Schober - Frank Gibson - PSU - electrical power supply - power pack - power supply unit - PERSON: Daniel Schober - sep:00093 - was power_pack, maps to SEP electrical_power_supply - power supply + A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time. + Daniel Schober + Frank Gibson + PSU + electrical power supply + power pack + power supply unit + PERSON: Daniel Schober + sep:00093 + was power_pack, maps to SEP electrical_power_supply + power supply @@ -88852,14 +99435,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - fluorometer - laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 + fluorometer + laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 - A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. - Allyson Lister - Kevin Lister - OBI - fluorometer + A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. + Allyson Lister + Kevin Lister + OBI + fluorometer @@ -88886,13 +99469,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - multispectral imaging flow cytometer + multispectral imaging flow cytometer - A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. - Melanie Courtot - MIFC - http://www.amnis.com/ - multispectral imaging flow cytometer + A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. + Melanie Courtot + MIFC + http://www.amnis.com/ + multispectral imaging flow cytometer @@ -88901,13 +99484,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microarray - An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. + microarray + An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. - A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. - Daniel Schober - PERSON: Chris Stoeckert - microarray + A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. + Daniel Schober + PERSON: Chris Stoeckert + microarray @@ -88916,16 +99499,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - DNA microarray - Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 + DNA microarray + Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 - A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. - PERSON: Daniel Schober - PERSON: Frank Gibson - DNA Chip - DNA-array - Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 - DNA microarray + A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. + PERSON: Daniel Schober + PERSON: Frank Gibson + DNA Chip + DNA-array + Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 + DNA microarray @@ -88934,13 +99517,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - protein microarray - The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. + protein microarray + The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. - A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. - Daniel Schober - PERSON: Daniel Schober - protein microarray + A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. + Daniel Schober + PERSON: Daniel Schober + protein microarray @@ -88955,12 +99538,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - droplet sorter + droplet sorter - A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. - OBI Instrument branch - OBI Instrument branch - droplet sorter + A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. + OBI Instrument branch + OBI Instrument branch + droplet sorter @@ -88969,13 +99552,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - water bath - A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. + water bath + A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. - A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). - Daniel Schober - PERSON: Daniel Schober - water bath + A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). + Daniel Schober + PERSON: Daniel Schober + water bath @@ -88984,13 +99567,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - oil bath - An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. + oil bath + An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. - An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). - Daniel Schober - PERSON: Daniel Schober - oil bath + An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). + Daniel Schober + PERSON: Daniel Schober + oil bath @@ -89005,13 +99588,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - digital-to-analog converter - A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. + digital-to-analog converter + A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. - A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. - Daniel Schober - PERSON: Daniel Schober - digital-to-analog converter + A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. + Daniel Schober + PERSON: Daniel Schober + digital-to-analog converter @@ -89032,13 +99615,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microtome - PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. + microtome + PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. - A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. - PERSON: Phillippe Rocca-Serra - PERSON: Daniel Schober - microtome + A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. + PERSON: Phillippe Rocca-Serra + PERSON: Daniel Schober + microtome @@ -89059,13 +99642,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microscope - PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 + microscope + PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 - A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) - PERSON: Phillippe Rocca-Serra - wikipedia - microscope + A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) + PERSON: Phillippe Rocca-Serra + wikipedia + microscope @@ -89080,13 +99663,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microscope slide - PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. + microscope slide + PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. - A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument - PERSON: Phillippe Rocca-Serra - OBI biomaterial branch - microscope slide + A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument + PERSON: Phillippe Rocca-Serra + OBI biomaterial branch + microscope slide @@ -89101,14 +99684,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - animal cage - PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. + animal cage + PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. - A processed material which has the function to define a bounded habitat which is amenable to keeping animals. - PERSON: Phillippe Rocca-Serra - laboratory cage - OBI biomaterial branch - animal cage + A processed material which has the function to define a bounded habitat which is amenable to keeping animals. + PERSON: Phillippe Rocca-Serra + laboratory cage + OBI biomaterial branch + animal cage @@ -89126,9 +99709,9 @@ Manual editing of automatically recorded data in an anesthesia information manag study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. - PERSON: Chris Stoeckert + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. @@ -89141,14 +99724,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - clinical study design - PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. + clinical study design + PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. - Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] - The definition needs to be extended to other things than simply patients - PlanAndPlannedProcess Branch - Clinical Research Glossary Version 4.0 CDICS glossary group - clinical study design + Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] + The definition needs to be extended to other things than simply patients + PlanAndPlannedProcess Branch + Clinical Research Glossary Version 4.0 CDICS glossary group + clinical study design @@ -89157,13 +99740,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - repeated measure design - PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. + repeated measure design + PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. - a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs - PlanAndPlannedProcess Branch - http://www.holah.karoo.net/experimentaldesigns.htm - repeated measure design + a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs + PlanAndPlannedProcess Branch + http://www.holah.karoo.net/experimentaldesigns.htm + repeated measure design @@ -89172,13 +99755,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - cross over design - PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. + cross over design + PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. - a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control - Philippe Rocca-Serra - (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) - cross over design + a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control + Philippe Rocca-Serra + (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) + cross over design @@ -89187,12 +99770,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - n-to-1 design + n-to-1 design - N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). - Philippe Rocca-Serra - Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) - n-to-1 design + N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). + Philippe Rocca-Serra + Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) + n-to-1 design @@ -89201,13 +99784,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - matched pairs design - PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. + matched pairs design + PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. - A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. - Philippe Rocca-Serra - http://www.holah.karoo.net/experimentaldesigns.htm - matched pairs design + A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. + Philippe Rocca-Serra + http://www.holah.karoo.net/experimentaldesigns.htm + matched pairs design @@ -89216,14 +99799,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - parallel group design - PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. + parallel group design + PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. - A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment - Philippe Rocca-Serra - independent measure design - http://www.holah.karoo.net/experimentaldesigns.htm - parallel group design + A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment + Philippe Rocca-Serra + independent measure design + http://www.holah.karoo.net/experimentaldesigns.htm + parallel group design @@ -89232,13 +99815,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - randomized complete block design - http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) + randomized complete block design + http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) - A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. - Philippe Rocca-Serra - http://www.tufts.edu/~gdallal/ranblock.htm - randomized complete block design + A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. + Philippe Rocca-Serra + http://www.tufts.edu/~gdallal/ranblock.htm + randomized complete block design @@ -89247,13 +99830,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - balanced incomplete block design - PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. + balanced incomplete block design + PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. - balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' - Philippe Rocca-Serra - http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html - balanced incomplete block design + balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' + Philippe Rocca-Serra + http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html + balanced incomplete block design @@ -89262,13 +99845,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - loop design - PMID: 12933549 + loop design + PMID: 12933549 - A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design - Philippe Rocca-Serra on behalf of MO - MO_912 - loop design + A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design + Philippe Rocca-Serra on behalf of MO + MO_912 + loop design @@ -89277,13 +99860,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - reference design - PMID: 12933549 + reference design + PMID: 12933549 - A reference experiment design type is where all samples are compared to a common reference. - Philippe Rocca-Serra on behalf of MO - MO_699 - reference design + A reference experiment design type is where all samples are compared to a common reference. + Philippe Rocca-Serra on behalf of MO + MO_699 + reference design @@ -89292,13 +99875,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - latin square design - PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. + latin square design + PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. - Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. - Philippe Rocca-Serra - Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and - latin square design + Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. + Philippe Rocca-Serra + Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and + latin square design @@ -89307,14 +99890,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - graeco latin square design - PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. + graeco latin square design + PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. - Greco-Latin square design is a study design which relates to Latin square design - Philippe Rocca-Serra - Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and - only 2 articles in pubmed ->probably irrelevant - graeco latin square design + Greco-Latin square design is a study design which relates to Latin square design + Philippe Rocca-Serra + Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and + only 2 articles in pubmed ->probably irrelevant + graeco latin square design @@ -89323,13 +99906,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - hyper graeco latin square design + hyper graeco latin square design - PRS to do - Philippe Rocca-Serra - Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and - no example found in pubmed->not in use in the community - hyper graeco latin square design + PRS to do + Philippe Rocca-Serra + Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and + no example found in pubmed->not in use in the community + hyper graeco latin square design @@ -89339,11 +99922,11 @@ Manual editing of automatically recorded data in an anesthesia information manag factorial design - PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. + PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. - factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. - Philippe Rocca-Serra - http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) + factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. + Philippe Rocca-Serra + http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) factorial design @@ -89353,13 +99936,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - 2x2 factorial design - PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. + 2x2 factorial design + PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. - a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors - Philippe Rocca-Serra - PMID: 17561240 - 2x2 factorial design + a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors + Philippe Rocca-Serra + PMID: 17561240 + 2x2 factorial design @@ -89368,12 +99951,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - fractional factorial design + fractional factorial design - A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run - Philippe Rocca-Serra - http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control - fractional factorial design + A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run + Philippe Rocca-Serra + http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control + fractional factorial design @@ -89382,13 +99965,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - dye swap design - PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. + dye swap design + PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. - An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip - Philippe Rocca-Serra on behalf of MO - MO_858 - dye swap design + An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip + Philippe Rocca-Serra on behalf of MO + MO_858 + dye swap design @@ -89397,12 +99980,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - replicate design + replicate design - A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. - Philippe Rocca-Serra on behalf of MO - MO_885 - replicate design + A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. + Philippe Rocca-Serra on behalf of MO + MO_885 + replicate design @@ -89411,13 +99994,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - self vs self design - PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. + self vs self design + PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. - A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. - Philippe Rocca-Serra on behalf of MO - MO_490 - self vs self design + A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. + Philippe Rocca-Serra on behalf of MO + MO_490 + self vs self design @@ -89426,13 +100009,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - time series design - PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. + time series design + PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. - Groups of assays that are related as part of a time series. - Philippe Rocca-Serra on behalf of MO - MO_887 - time series design + Groups of assays that are related as part of a time series. + Philippe Rocca-Serra on behalf of MO + MO_887 + time series design @@ -89594,7 +100177,7 @@ defines and states the requirements (positive or negative) for an entity to be c adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient is process in which a material substance is added to a cell culture - renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms + renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms Bjoern Peters IEDB adding substance to cell culture @@ -89625,10 +100208,10 @@ defines and states the requirements (positive or negative) for an entity to be c tumor grading - An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. - Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney - grading of tumor - OBI branch derived; submitted by MO + An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. + Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney + grading of tumor + OBI branch derived; submitted by MO tumor grading @@ -89668,10 +100251,10 @@ defines and states the requirements (positive or negative) for an entity to be c performing a clinical assessment - A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. - PlanAndPlannedProcess Branch - clinical diagnosis - OBI branch derived + A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. + PlanAndPlannedProcess Branch + clinical diagnosis + OBI branch derived performing a clinical assessment @@ -89742,7 +100325,7 @@ defines and states the requirements (positive or negative) for an entity to be c enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. - As with group assignment, should the specified output here be an organism which bears a role + As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch @@ -89832,7 +100415,7 @@ defines and states the requirements (positive or negative) for an entity to be c A protocol application in which an organism is intentionally put to death difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing. Jennifer Fostel - Philippe Rocca-Serra + Philippe Rocca-Serra death status type euthanisia life termination @@ -89903,17 +100486,17 @@ defines and states the requirements (positive or negative) for an entity to be c administering substance in vivo - Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells + Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally - A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 + A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 Different routes and means of administration should go as children underneath this Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/ needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. Bjoern Peters - Person:Bjoern Peters + Person:Bjoern Peters IEDB administering substance in vivo @@ -89949,10 +100532,10 @@ https://sourceforge.net/p/obi/obi-terms/738/ acquisition - Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. + Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. the planned process of gaining possession of a continuant - 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. + 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule' @@ -89994,10 +100577,10 @@ Relates to the creation of a class 'selection rule' Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. An acquisition in which possession of a material entity is gained. - The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation + The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation This excludes processes that create or change materials, such as material transformations. Bjoern Peters, Alan Ruttenberg, Helen Parkinson - material procurement + material procurement IEDB material acquisition @@ -90071,7 +100654,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ An acquisition in which possession of information is gained. This excludes processes that create or change information, such as assays and data transformations. Bjoern Peters - data collection + data collection OBI branch derived information acquisition @@ -90142,8 +100725,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ group assignment is a process which has an organism as specified input and during which a role is assigned Philippe Rocca-Serra - cohort assignment - study assignment + cohort assignment + study assignment OBI Plan group assignment @@ -90178,7 +100761,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ 2 - pooling specimens + pooling specimens http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points physical combination of several instances of like material @@ -90219,11 +100802,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ assay detecting a molecular label - Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present + Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present - An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached - Matthew Brush - OBI developer call, 3-12-12 + An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached + Matthew Brush + OBI developer call, 3-12-12 assay detecting a molecular label @@ -90303,14 +100886,14 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ histological assay - the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated + the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated - An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. - Adam Witney - Helen Parkinson - histology - histopathology - OBI branch derived + An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. + Adam Witney + Helen Parkinson + histology + histopathology + OBI branch derived histological assay @@ -90496,11 +101079,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ substance detection assay - the detection of phycoerytherin by means of flow cytometry + the detection of phycoerytherin by means of flow cytometry - An assay that detects a specified substance - Kevin Clancy - OBI branch derived + An assay that detects a specified substance + Kevin Clancy + OBI branch derived substance detection assay @@ -90523,11 +101106,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ longitudinal mass measurement assay - The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection + The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection - An assay that measures the mass of a material at two or more time points - Helen Parkinson - OBI branch derived + An assay that measures the mass of a material at two or more time points + Helen Parkinson + OBI branch derived longitudinal mass measurement assay @@ -90587,7 +101170,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) - It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. + It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope PERSON:Kevin Clancy OBI branch derived @@ -90703,12 +101286,12 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ enzyme-linked immunospot assay - Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. + Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. - A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. - IEDB - ELISPOT assay - IEDB + A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. + IEDB + ELISPOT assay + IEDB enzyme-linked immunospot assay @@ -90858,7 +101441,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing PlanAndPlannedProcess Branch - cell culture passaging + cell culture passaging OBI branch derived An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. cell culture splitting @@ -90899,7 +101482,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay PERSON:Matthew Brush - labeling + labeling OBI developer call, 3-12-12 addition of molecular label @@ -90949,7 +101532,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - synthesis + synthesis making cDNA from nucleotides using RNA as a template the construction of a biomaterial from simpler biomaterials @@ -91090,11 +101673,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ 3D structure determination assay - The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. + The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. - An assay that determines the 3-dimensional configuration of an input material. - IEDB - IEDB + An assay that determines the 3-dimensional configuration of an input material. + IEDB + IEDB 3D structure determination assay @@ -91252,11 +101835,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ sequencing assay - The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template + The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template - An assay the uses chemical or biochemical means to infer the sequence of a biomaterial - PlanAndPlannedProcess Branch - OBI branch derived + An assay the uses chemical or biochemical means to infer the sequence of a biomaterial + PlanAndPlannedProcess Branch + OBI branch derived sequencing assay @@ -91266,7 +101849,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - vector mediated amplification + vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. The process of creating a copy of some biological entity in cell culture @@ -91308,7 +101891,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input PERSON:Kevin Clancy - Philippe Rocca-Serra + Philippe Rocca-Serra OBI branch derived DNA polymerase amplification @@ -91624,7 +102207,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ vector mediated expression - Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity. + Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity. vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector needs defined relationship to cell culture @@ -91683,7 +102266,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material pa_branch (Alan, Randi, Kevin, Jay, Bjoern) - molecular cloning + molecular cloning OBI branch derived recombinant vector cloning @@ -91696,9 +102279,9 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ obsolete_defined processes - Place holder class, see editor note - PlanAndPlannedProcess Branch - OBI branch derived + Place holder class, see editor note + PlanAndPlannedProcess Branch + OBI branch derived obsolete_defined processes true @@ -91835,9 +102418,9 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra GROUP: CEBS - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch cell pellet @@ -91892,14 +102475,14 @@ addition of has_role restriction cell lysate - The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 + The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 a cell lysate is a material entity which is output of a cell lysis process PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process PERSON: Susanna Sansone lysate - lysed material + lysed material GROUP: PSI cell lysate @@ -91952,7 +102535,7 @@ Possible ecological risks of transgenic organism release when transgenes affect a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra GROUP:IEDB transgenic organism @@ -91981,7 +102564,7 @@ Possible ecological risks of transgenic organism release when transgenes affect A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra whole mount sample GROUP: OBI PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity @@ -92017,7 +102600,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - epitope + epitope a material entity bearing the epitope role IEDB @@ -92033,9 +102616,9 @@ Possible ecological risks of transgenic organism release when transgenes affect obsolete_occurrence of disease - An occurrence of disease is a process involving pathologic changes within an organism - IEDB - IEDB + An occurrence of disease is a process involving pathologic changes within an organism + IEDB + IEDB obsolete_occurrence of disease true @@ -92081,7 +102664,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - host exposure to infectious agent + host exposure to infectious agent a process in which an infectious agent comes into physical contact with a host organism. IEDB @@ -92111,7 +102694,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - administration in vivo with infectious agent + administration in vivo with infectious agent is an administration of an infectious agent to a host organism IEDB @@ -92153,7 +102736,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - occurrence of infectious disease + occurrence of infectious disease Is an occurrence of a disease caused by an infection IEDB @@ -92173,11 +102756,11 @@ Possible ecological risks of transgenic organism release when transgenes affect - disposition to cause an allergic reaction + disposition to cause an allergic reaction The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease. IEDB - allergenic disposition + allergenic disposition IEDB disposition to cause an allergic reaction @@ -92194,7 +102777,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - allergic reaction + allergic reaction an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) IEDB @@ -92220,7 +102803,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - occurrence of allergy + occurrence of allergy The process of an allergic disease occurring in an organism. IEDB @@ -92236,21 +102819,37 @@ Possible ecological risks of transgenic organism release when transgenes affect - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-2 production by T cells @@ -92286,7 +102885,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - epitope binding by adaptive immune receptor + epitope binding by adaptive immune receptor is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. IEDB @@ -92306,7 +102905,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - Immunization in vivo + Immunization in vivo Process of administering an object playing the role of immunogen to a living organism IEDB @@ -92340,7 +102939,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - adaptive immune effector function + adaptive immune effector function A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience. IEDB @@ -92354,9 +102953,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - living with infected household contact + living with infected household contact - a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent + a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent IEDB IEDB living with infected household contact @@ -92368,9 +102967,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - living in endemic area + living in endemic area - a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely + a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely IEDB IEDB living in endemic area @@ -92382,9 +102981,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - pathogen release in laboratory accident + pathogen release in laboratory accident - a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent + a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent IEDB IEDB pathogen release in laboratory accident @@ -92420,7 +103019,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - Immunization in vitro + Immunization in vitro Process of administering an object playing the role of immunogen to a cell culture IEDB @@ -92446,7 +103045,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - infection process + infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB @@ -92469,7 +103068,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - adaptive immune receptor + adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB @@ -92489,7 +103088,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - immunogen + immunogen a material entity bearing the immunogen role IEDB @@ -92540,7 +103139,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - environmental exposure to infectious agent + environmental exposure to infectious agent Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent IEDB @@ -92565,11 +103164,11 @@ Possible ecological risks of transgenic organism release when transgenes affect - host of immune response - A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. + host of immune response + A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. An organism in which an immune response process occurs. - In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation. + In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation. IEDB IEDB host of immune response @@ -92581,9 +103180,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - 293-T cell line + 293-T cell line - A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. + A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5008.html @@ -92596,9 +103195,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - C1R cell line + C1R cell line - A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). + A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). IEDB IEDB C1R cell line @@ -92626,7 +103225,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - experimental infection of cell culture + experimental infection of cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture IEDB @@ -92640,9 +103239,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - EL-4 cell line + EL-4 cell line - A cell line derived from mouse (C57BL/6N) lymphoma cells. + A cell line derived from mouse (C57BL/6N) lymphoma cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1160.html @@ -92655,9 +103254,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - HeLa cell culture + HeLa cell culture - A cell line derived from human cervical cancer cells. + A cell line derived from human cervical cancer cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1597.html @@ -92670,9 +103269,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - JAWS II cell line + JAWS II cell line - A cell line derived from mouse dendritic cells. + A cell line derived from mouse dendritic cells. IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology @@ -92691,7 +103290,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - antigen + antigen is a material entity that has the antigen role IEDB @@ -92705,9 +103304,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - Jurkat cell line + Jurkat cell line - A cell line derived from human T cells. + A cell line derived from human T cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5296.html @@ -92720,9 +103319,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - JY cell line + JY cell line - The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) + The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) IEDB IEDB JY cell line @@ -92736,36 +103335,30 @@ Possible ecological risks of transgenic organism release when transgenes affect - + + + + + - - - - - - - - - - - + - + assay measuring binding of a T cell epitope:MHC:TCR complex - An immune epitope assay that detects T cell epitope recognition. - IEDB - IEDB - T cell binding|any method + A T cell epitope assay that measures the binding of T cell receptor to an epitope. + IEDB + IEDB + T cell binding|any method assay measuring binding of a T cell epitope:MHC:TCR complex @@ -92775,9 +103368,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - RMA cell line + RMA cell line - A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface. + A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface. IEDB IEDB RMA cell line @@ -92789,9 +103382,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - T2 cell line + T2 cell line - A human T-B lymphoblastoid hybrid cell line + A human T-B lymphoblastoid hybrid cell line IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology @@ -92804,7 +103397,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - infectious disease + infectious disease is a disease caused by an infectious agent IEDB @@ -92835,9 +103428,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen + lymph node cell specimen - A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. + A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB lymph node cell specimen @@ -92860,9 +103453,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - cultured adherent cell population + cultured adherent cell population - A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role. + A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role. MHB 3-27-13: Following CLO alignment efforts, propose to update definition to read: "A cultured cell population comprised of cells that are able to grow attached to a solid substrate provided by tissue culture flasks or plates". The current definition seems to describe a more specific type of adherent culture of immunological origin as needed by IEDB. MHB 3-5-13: Need to review axiom on this class in light of clarification that it refers to a cell line sample, and not an entire line. Not every population of adhernet cells is the output of an isolation process. @@ -92889,9 +103482,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured PBMC cell population + cultured PBMC cell population - A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). + A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). IEDB PBMC cell culture sample IEDB @@ -92910,11 +103503,11 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - disposition to be bound by an adaptive immune receptor + disposition to be bound by an adaptive immune receptor Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. IEDB - epitope disposition + epitope disposition IEDB disposition to be bound by an adaptive immune receptor @@ -92925,7 +103518,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - organ harvesting + organ harvesting The process of removing an organ from its source organism IEDB @@ -92960,9 +103553,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD3+ T cell population + cultured CD3+ T cell population - A T cell population characterized by expressing the CD3 molecule on its surface. + A T cell population characterized by expressing the CD3 molecule on its surface. IEDB CD3+ T cell culture sample IEDB @@ -93000,9 +103593,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD3- T cell population + cultured CD3- T cell population - A T cell population characterized by not expressing the CD3 molecule on its surface. + A T cell population characterized by not expressing the CD3 molecule on its surface. IEDB CD3- T cell culture sample IEDB @@ -93015,7 +103608,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - allergy + allergy is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect IEDB @@ -93054,9 +103647,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD4- T cell population + cultured CD4- T cell population - A T cell population characterized by not expressing the CD4 molecule on its surface. + A T cell population characterized by not expressing the CD4 molecule on its surface. IEDB CD4- T cell culture sample IEDB @@ -93094,9 +103687,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD8- T cell population + cultured CD8- T cell population - A T cell population characterized by not expressing the CD8 molecule on its surface. + A T cell population characterized by not expressing the CD8 molecule on its surface. IEDB CD8- T cell culture sample IEDB @@ -93143,9 +103736,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD4-/CD8- T cell population + cultured CD4-/CD8- T cell population - A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. + A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. IEDB CD4-/CD8- T cell culture sample IEDB @@ -93158,7 +103751,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cancer + cancer A disease characterized by abnormal and uncontrolled cell division IEDB @@ -93172,7 +103765,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - autoimmune disease + autoimmune disease Is a disease characterized by an immune response of an organism against parts of itself IEDB @@ -93188,9 +103781,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it obsolete_disease - placeholder to be imported from disease ontology - IEDB - IEDB + placeholder to be imported from disease ontology + IEDB + IEDB obsolete_disease @@ -93215,7 +103808,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-2 release by T cells + epitope specific IL-2 release by T cells A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope. IEDB @@ -93276,7 +103869,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - MHC:epitope complex binding to TCR + MHC:epitope complex binding to TCR a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. IEDB @@ -93292,21 +103885,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISPOT + An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISPOT ELISPOT assay measuring epitope specific interferon-gamma production by T cells @@ -93316,9 +103925,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - exposure resulting in immune reactivity + exposure resulting in immune reactivity - a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity + a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity IEDB IEDB exposure resulting in immune reactivity @@ -93330,7 +103939,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - immunogen role + immunogen role any entity capable of eliciting an immune response when introduced to components of the immune system IEDB @@ -93357,10 +103966,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - host of immune response role + host of immune response role is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host. - 03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO. + 03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO. IEDB IEDB host of immune response role @@ -93394,7 +104003,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - effector T cell function + effector T cell function The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex. IEDB @@ -93424,13 +104033,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - antigen presentation function + antigen presentation function a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface. IEDB APC IEDB - should add a reference to the antigen processing and presentation process. + should add a reference to the antigen processing and presentation process. antigen presentation function @@ -93440,7 +104049,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - restricting MHC role + restricting MHC role The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. IEDB @@ -93454,14 +104063,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - donor - A T cell line from a PPD(+) donor. + donor + A T cell line from a PPD(+) donor. A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB - donor role + donor role IEDB - Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. + Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. donor @@ -93471,10 +104080,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - immune epitope carrier role + immune epitope carrier role A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity. - 03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence. + 03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence. IEDB IEDB immune epitope carrier role @@ -93498,11 +104107,11 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - adjuvant role + adjuvant role Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. IEDB - adjuvent role + adjuvent role IEDB adjuvant role @@ -93519,7 +104128,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - disposition to infect an organism + disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB @@ -93599,8 +104208,8 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - immunization - Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). + immunization + Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope. IEDB @@ -93620,7 +104229,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - blood harvesting + blood harvesting A material separation where blood is taken from an organism. IEDB @@ -93634,9 +104243,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - L cell line + L cell line - A cell line derived from mouse fibroblasts. + A cell line derived from mouse fibroblasts. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl3075.html @@ -93670,13 +104279,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured antigen presenting cell population - A culture of PBMCs. A culture of Hela cells. + cultured antigen presenting cell population + A culture of PBMCs. A culture of Hela cells. - a cell culture including cells that have an antigen presentation function + a cell culture including cells that have an antigen presentation function antigen presenting cell culture sample - IEDB - cultured antigen presenting cell population + IEDB + cultured antigen presenting cell population @@ -93706,14 +104315,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured effector T cell population - A culture of cytotoxic CD8+ T cells. + cultured effector T cell population + A culture of cytotoxic CD8+ T cells. - A cell culture including cells that have an effector T cell function + A cell culture including cells that have an effector T cell function culture of effector T cells effector T cell culture sample - IEDB - cultured effector T cell population + IEDB + cultured effector T cell population @@ -93728,14 +104337,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - material to be added - A mixture of peptides that is being added into a cell culture. + material to be added + A mixture of peptides that is being added into a cell culture. - a material that is added to another one in a material combination process - 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export - 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes - IEDB - material to be added + a material that is added to another one in a material combination process + 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export + 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes + IEDB + material to be added @@ -93750,13 +104359,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - target of material addition - A cell culture into which a mixture of peptides is being added. + target of material addition + A cell culture into which a mixture of peptides is being added. - A material entity into which another is being added in a material combinatino process - 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. - IEDB - target of material addition + A material entity into which another is being added in a material combinatino process + 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. + IEDB + target of material addition @@ -93765,7 +104374,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - environmental proximity to infectious agent + environmental proximity to infectious agent Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result IEDB @@ -93779,9 +104388,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - contact to pathogen carrying biological vector + contact to pathogen carrying biological vector - a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result + a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result IEDB IEDB contact to pathogen carrying biological vector @@ -93810,9 +104419,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen + splenocyte specimen - A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. + A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB splenocyte specimen @@ -93824,9 +104433,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - P815 cell line + P815 cell line - A cell line derived from mouse mastocytoma. + A cell line derived from mouse mastocytoma. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5244.html @@ -93845,7 +104454,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - assay antigen role + assay antigen role Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below IEDB @@ -93859,7 +104468,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - pathologic process + pathologic process abnormal, harmful processes caused by or associated with a disease IEDB @@ -93875,7 +104484,11 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + @@ -93889,13 +104502,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + assay measuring qualitative binding of a T cell epitope:MHC:TCR complex - A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|binding assay - assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|binding assay + assay measuring qualitative binding of a T cell epitope:MHC:TCR complex @@ -93906,7 +104519,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -93946,10 +104559,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it assay measuring MHC ligand processing and presentation - A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. - IEDB - IEDB - ligand presentation|any method + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. + IEDB + IEDB + ligand presentation|any method assay measuring MHC ligand processing and presentation @@ -93961,27 +104574,17 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + - - - - - - - - - - - - - - - + @@ -93991,10 +104594,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it assay measuring binding of a MHC:ligand complex - A MHC ligand assay that detects the binding of a ligand to an MHC molecule. - IEDB - IEDB - MHC binding|binding assay + A MHC ligand assay that detects the binding of a ligand to an MHC molecule. + IEDB + IEDB + MHC binding|any method assay measuring binding of a MHC:ligand complex @@ -94006,36 +104609,30 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + + + - - - - - - - - - - - + - + assay measuring binding of a B cell epitope:antibody complex - An immune epitope assay that detects B cell epitope recognition. - IEDB - IEDB - antibody binding|any method + A B cell epitope assay that measures the binding of an antibody receptor to an epitope. + IEDB + IEDB + antibody binding|any method assay measuring binding of a B cell epitope:antibody complex @@ -94044,12 +104641,59 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immune epitope assay - An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event - IEDB - IEDB + An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event. + IEDB + IEDB immune epitope assay immune epitope assay @@ -94059,25 +104703,40 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - + + + + - - + + + + + + + + + + + + + + + + + - - - - biological activity assay measuring epitope specific cytokine production by T cells + + + + + assay measuring epitope specific cytokine production by T cells - A T cell epitope dependent biological activity assay that detects cytokine production. - IEDB - IEDB - cytokine release|biological activity - biological activity assay measuring epitope specific cytokine production by T cells + A T cell epitope assay that detects cytokine production by T cells. + IEDB + IEDB + cytokine release|biological activity + assay measuring epitope specific cytokine production by T cells @@ -94108,10 +104767,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it biological activity assay measuring epitope specific T cell killing - A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. - IEDB - IEDB - cytotoxicity|biological activity + A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. + IEDB + IEDB + cytotoxicity|biological activity biological activity assay measuring epitope specific T cell killing @@ -94143,10 +104802,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it biological activity assay measuring epitope specific proliferation of T cells - A T cell epitope dependent biological activity assay that detects T cell proliferation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - proliferation|biological activity + A T cell epitope dependent biological activity assay that detects T cell proliferation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + proliferation|biological activity biological activity assay measuring epitope specific proliferation of T cells @@ -94156,13 +104815,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - CD8 receptor + CD8 receptor - A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. - This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. - CD8 - WEB: http://en.wikipedia.org/wiki/CD8 - CD8 receptor + A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. + This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. + CD8 + WEB: http://en.wikipedia.org/wiki/CD8 + CD8 receptor @@ -94184,10 +104843,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 51 chromium assay measuring epitope specific T cell killing - A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. - IEDB - IEDB - cytotoxicity|51 chromium + A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. + IEDB + IEDB + cytotoxicity|51 chromium 51 chromium assay measuring epitope specific T cell killing @@ -94199,21 +104858,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISA + An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISA ELISA measuring epitope specific interferon-gamma production by T cells @@ -94225,21 +104900,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISA ELISA measuring epitope specific interleukin-2 production by T cells @@ -94251,21 +104942,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-4 production by T cells - An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISA ELISA measuring epitope specific interleukin-4 production by T cells @@ -94277,21 +104984,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-5 production by T cells - An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ELISA ELISA measuring epitope specific interleukin-5 production by T cells @@ -94303,10 +105026,25 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + @@ -94315,10 +105053,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it ELISA measuring epitope specific tumor necrosis factor production by T cells - A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ELISA + An enzyme-linked immunosorbent assay that detects tumor necrosis factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|ELISA ELISA measuring epitope specific tumor necrosis factor production by T cells @@ -94330,21 +105068,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-10 production by T cells - An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISA ELISA measuring epitope specific interleukin-10 production by T cells @@ -94356,21 +105110,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|ELISA + An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|ELISA ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -94382,21 +105152,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-6 production by T cells - An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ELISA ELISA measuring epitope specific interleukin-6 production by T cells @@ -94408,21 +105194,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-13 production by T cells - An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISA ELISA measuring epitope specific interleukin-13 production by T cells @@ -94434,21 +105236,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-12 production by T cells - An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ELISA ELISA measuring epitope specific interleukin-12 production by T cells @@ -94460,21 +105278,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-1 beta production by T cells - An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|ELISA ELISA measuring epitope specific interleukin-1 beta production by T cells @@ -94486,21 +105320,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-17 production by T cells - An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ELISA ELISA measuring epitope specific interleukin-17 production by T cells @@ -94512,21 +105362,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-18 production by T cells - An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISA + An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ELISA ELISA measuring epitope specific interleukin-18 production by T cells @@ -94538,21 +105404,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-4 production by T cells - An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-4 production by T cells @@ -94564,10 +105446,25 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + @@ -94576,10 +105473,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells - A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. - IEDB - IEDB - TNFa release|ELISPOT + An enzyme-linked immunospot assay that detects tumor necrosis factor production by T cells. + IEDB + IEDB + TNFa release|ELISPOT ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells @@ -94591,21 +105488,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-10 production by T cells - An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-10 production by T cells @@ -94617,21 +105530,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-13 production by T cells - An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISPOT + An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-13 production by T cells @@ -94643,21 +105572,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells - An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ICS + A flow cytometry assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ICS intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells @@ -94669,21 +105614,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells - An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ICS + A flow cytometry assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells @@ -94695,10 +105656,25 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + @@ -94707,10 +105683,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells - A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ICS + A flow cytometry assay that detects tumor necrosis factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells @@ -94722,21 +105698,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells - An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ICS + A flow cytometry assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells @@ -94748,21 +105740,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells - An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ICS + A flow cytometry assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells @@ -94774,21 +105782,37 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - - + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells - An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ICS + A flow cytometry assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells @@ -94800,7 +105824,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -94824,8 +105848,17 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - + + + + + + + + + + + @@ -94834,10 +105867,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex - A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|multimer/tetramer + A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|multimer/tetramer MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex @@ -94860,10 +105893,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 3H-thymidine assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. - IEDB - IEDB - proliferation|3H-thymidine + A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. + IEDB + IEDB + proliferation|3H-thymidine 3H-thymidine assay measuring epitope specific proliferation of T cells @@ -94886,10 +105919,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it BrdU assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. - IEDB - IEDB - proliferation|BrdU + A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. + IEDB + IEDB + proliferation|BrdU BrdU assay measuring epitope specific proliferation of T cells @@ -94910,7 +105943,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific T cell proliferation + epitope specific T cell proliferation A biological process where T cells proliferate resulting from the recognition of a T cell epitope. IEDB @@ -94936,7 +105969,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific GM-CSF release by T cells + epitope specific GM-CSF release by T cells A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope. IEDB @@ -94962,7 +105995,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IFN-g release by T cells + epitope specific IFN-g release by T cells A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. IEDB @@ -94988,7 +106021,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-10 release by T cells + epitope specific IL-10 release by T cells A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope. IEDB @@ -95014,7 +106047,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-12 release by T cells + epitope specific IL-12 release by T cells A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope. IEDB @@ -95040,7 +106073,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-13 release by T cells + epitope specific IL-13 release by T cells A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope. IEDB @@ -95066,7 +106099,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-17 release by T cells + epitope specific IL-17 release by T cells A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope. IEDB @@ -95092,7 +106125,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-18 release by T cells + epitope specific IL-18 release by T cells A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope. IEDB @@ -95118,7 +106151,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-1b release by T cells + epitope specific IL-1b release by T cells A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope. IEDB @@ -95144,7 +106177,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-4 release by T cells + epitope specific IL-4 release by T cells A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope. IEDB @@ -95169,13 +106202,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - allergen - Birch pollen is an allergen + allergen + Birch pollen is an allergen - A material entity bearing the disposition to cause an allergic reaction - IEDB - IEDB - allergen + A material entity bearing the disposition to cause an allergic reaction + IEDB + IEDB + allergen @@ -95196,7 +106229,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-5 release by T cells + epitope specific IL-5 release by T cells A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope. IEDB @@ -95222,7 +106255,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-6 release by T cells + epitope specific IL-6 release by T cells A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope. IEDB @@ -95247,7 +106280,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific killing by T cells + epitope specific killing by T cells A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell. IEDB @@ -95273,7 +106306,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific TNF release by T cells + epitope specific TNF release by T cells A biological process where T cells produce TNF resulting from the recognition of a T cell epitope. IEDB @@ -95309,12 +106342,12 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it assay detecting IFN-gamma production - An IFN-g ELISPOT is an assay detecting ifn-gamma production + An IFN-g ELISPOT is an assay detecting ifn-gamma production - An assay that determines information about the production of the cytokine interferon gamma - Bjoern Peters - IFNg release - IEDB + An assay that determines information about the production of the cytokine interferon gamma + Bjoern Peters + IFNg release + IEDB assay detecting IFN-gamma production @@ -95324,15 +106357,15 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - direct submission to IEDB - The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. + direct submission to IEDB + The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. The content of that report on the IEDB website is here: http://iedb.org/refId/1013357 - A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) - PERSON: Bjoern Peters - IEDB - direct submission to IEDB + A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) + PERSON: Bjoern Peters + IEDB + direct submission to IEDB @@ -95381,11 +106414,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 uterine cervix specimen - A specimen that is derived from some uterine cervix - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some uterine cervix + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 uterine cervix specimen @@ -95416,11 +106449,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 urethra specimen - A specimen that is derived from some urethra - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some urethra + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 urethra specimen @@ -95451,11 +106484,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cervical mucus specimen - A specimen that is derived from some cervical mucus - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some cervical mucus + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 cervical mucus specimen @@ -95486,11 +106519,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 throat specimen - A specimen that is derived from some throat - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some throat + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 throat specimen @@ -95521,11 +106554,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 eye specimen - A specimen that is derived from some eye - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some eye + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 eye specimen @@ -95556,11 +106589,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 respiratory system specimen - A specimen that is derived from some respiratory system - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some respiratory system + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 respiratory system specimen @@ -95591,11 +106624,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 upper respiratory tract specimen - A specimen that is derived from some upper respiratory tract - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some upper respiratory tract + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 upper respiratory tract specimen @@ -95626,11 +106659,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 nasopharynx specimen - A specimen that is derived from some nasopharynx - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some nasopharynx + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 nasopharynx specimen @@ -95661,11 +106694,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 semen specimen - A specimen that is derived from some semen - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some semen + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 semen specimen @@ -95696,11 +106729,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bodily fluid specimen - A specimen that is derived from some bodily fluid - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some bodily fluid + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen @@ -95731,11 +106764,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chorionic villus specimen - A specimen that is derived from some chorionic villus - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some chorionic villus + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 chorionic villus specimen @@ -95766,11 +106799,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 meconium specimen - A specimen that is derived from some meconium - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some meconium + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 meconium specimen @@ -95801,11 +106834,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 umbilical cord blood specimen - A specimen that is derived from some umbilical cord blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some umbilical cord blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 umbilical cord blood specimen @@ -95836,11 +106869,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood specimen - A specimen that is derived from some arterial blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some arterial blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 arterial blood specimen @@ -95871,11 +106904,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood specimen - A specimen that is derived from some venous blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some venous blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 venous blood specimen @@ -95906,11 +106939,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 capillary blood specimen - A specimen that is derived from some capillary blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some capillary blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 capillary blood specimen @@ -95943,11 +106976,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 erythrocyte specimen - A specimen that is derived from some erythrocytes - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some erythrocytes + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 erythrocyte specimen @@ -95980,11 +107013,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 reticulocyte specimen - A specimen that is derived from some reticulocytes - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some reticulocytes + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 reticulocyte specimen @@ -96017,11 +107050,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 leukocyte specimen - A specimen that is derived from some leukocytes - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 + A specimen that is derived from some leukocytes + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 leukocyte specimen @@ -96062,10 +107095,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 carbon dioxide assay @@ -96106,10 +107139,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 sodium(1+) assay - An analyte assay that measures the abundance of sodium(1+) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium(1+) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 sodium(1+) assay @@ -96150,10 +107183,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 creatinine assay - An analyte assay that measures the abundance of creatinine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 creatinine assay @@ -96194,10 +107227,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 potassium(1+) assay - An analyte assay that measures the abundance of potassium(1+) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium(1+) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 potassium(1+) assay @@ -96220,10 +107253,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basophil count assay - A cytometry assay that measures the count of basophils - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of basophils + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basophil count assay @@ -96246,10 +107279,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 neutrophil count assay - A cytometry assay that measures the count of neutrophils - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of neutrophils + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 neutrophil count assay @@ -96272,10 +107305,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 eosinophil count assay - A cytometry assay that measures the count of eosinophils - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of eosinophils + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 eosinophil count assay @@ -96298,10 +107331,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lymphocyte count assay - A cytometry assay that measures the count of lymphocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of lymphocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lymphocyte count assay @@ -96324,10 +107357,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 monocyte count assay - A cytometry assay that measures the count of monocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of monocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 monocyte count assay @@ -96368,10 +107401,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chloride assay - An analyte assay that measures the abundance of chloride - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chloride assay @@ -96394,10 +107427,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 erythrocyte count assay - A cytometry assay that measures the count of erythrocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of erythrocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 erythrocyte count assay @@ -96420,10 +107453,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 platelet count assay - A cytometry assay that measures the count of platelets - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of platelets + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 platelet count assay @@ -96446,10 +107479,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 leukocyte count assay - A cytometry assay that measures the count of leukocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of leukocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 leukocyte count assay @@ -96490,10 +107523,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hemoglobin assay - An analyte assay that measures the abundance of hemoglobin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hemoglobin assay @@ -96534,10 +107567,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 phosphate ion assay - An analyte assay that measures the abundance of phosphate ion - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of phosphate ion + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 phosphate ion assay @@ -96578,10 +107611,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 alanine aminotransferase assay @@ -96622,10 +107655,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 alkaline phosphatase (human) assay - An analyte assay that measures the abundance of alkaline phosphatase (human) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alkaline phosphatase (human) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 alkaline phosphatase (human) assay @@ -96666,10 +107699,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bilirubin IXalpha assay - An analyte assay that measures the abundance of bilirubin IXalpha - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin IXalpha + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bilirubin IXalpha assay @@ -96710,10 +107743,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 aspartate aminotransferase (human) assay - An analyte assay that measures the abundance of aspartate aminotransferase (human) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of aspartate aminotransferase (human) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 aspartate aminotransferase (human) assay @@ -96754,10 +107787,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 glucose assay - An analyte assay that measures the abundance of glucose - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 glucose assay @@ -96798,10 +107831,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 magnesium cation assay - An analyte assay that measures the abundance of magnesium cation - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of magnesium cation + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 magnesium cation assay @@ -96842,10 +107875,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 albumin assay - An analyte assay that measures the abundance of albumin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 albumin assay @@ -96886,10 +107919,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 protein assay - An analyte assay that measures the abundance of protein - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 protein assay @@ -96930,10 +107963,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 calcium cation assay - An analyte assay that measures the abundance of calcium cation - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium cation + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 calcium cation assay @@ -96974,10 +108007,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 creatine kinase assay - An analyte assay that measures the abundance of creatine kinase - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatine kinase + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 creatine kinase assay @@ -97000,10 +108033,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 nucleate erythrocyte count assay - A cytometry assay that measures the count of nucleate erythrocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of nucleate erythrocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 nucleate erythrocyte count assay @@ -97026,10 +108059,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 segmented neutrophil of bone marrow count assay - A cytometry assay that measures the count of segmented neutrophil of bone marrows - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of segmented neutrophil of bone marrows + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 segmented neutrophil of bone marrow count assay @@ -97057,10 +108090,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lactate dehydrogenase complex assay - An assay that measures lactate dehydrogenase complex - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactate dehydrogenase complex + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lactate dehydrogenase complex assay @@ -97101,10 +108134,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 triglyceride assay - An analyte assay that measures the abundance of triglyceride - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of triglyceride + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 triglyceride assay @@ -97145,10 +108178,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 high-density lipoprotein cholesterol assay - An analyte assay that measures the abundance of high-density lipoprotein cholesterol - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of high-density lipoprotein cholesterol + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 high-density lipoprotein cholesterol assay @@ -97189,10 +108222,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cholesterol assay - An analyte assay that measures the abundance of cholesterol - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of cholesterol + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cholesterol assay @@ -97233,10 +108266,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 low-density lipoprotein cholesterol assay - An analyte assay that measures the abundance of low-density lipoprotein cholesterol - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of low-density lipoprotein cholesterol + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 low-density lipoprotein cholesterol assay @@ -97277,10 +108310,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 thyroid stimulating hormone assay - An analyte assay that measures the abundance of thyroid stimulating hormone - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of thyroid stimulating hormone + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 thyroid stimulating hormone assay @@ -97321,10 +108354,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 prostate-specific antigen assay - An analyte assay that measures the abundance of prostate-specific antigen - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of prostate-specific antigen + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 prostate-specific antigen assay @@ -97365,10 +108398,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 thyroxine assay - An analyte assay that measures the abundance of thyroxine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of thyroxine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 thyroxine assay @@ -97409,10 +108442,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 elemental oxygen assay - An analyte assay that measures the abundance of elemental oxygen - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of elemental oxygen + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 elemental oxygen assay @@ -97453,10 +108486,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 folic acids assay - An analyte assay that measures the abundance of folic acids - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of folic acids + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 folic acids assay @@ -97479,10 +108512,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 reticulocyte count assay - A cytometry assay that measures the count of reticulocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of reticulocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 reticulocyte count assay @@ -97510,10 +108543,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 osmolality assay - An assay that measures osmolality - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures osmolality + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 osmolality assay @@ -97554,10 +108587,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 methemoglobin assay - An analyte assay that measures the abundance of methemoglobin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of methemoglobin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 methemoglobin assay @@ -97585,10 +108618,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cytosolic creatine kinase complex, MB-type assay - An assay that measures cytosolic creatine kinase complex, MB-type - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures cytosolic creatine kinase complex, MB-type + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cytosolic creatine kinase complex, MB-type assay @@ -97616,10 +108649,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 rac-lactic acid assay - An assay that measures rac-lactic acid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures rac-lactic acid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 rac-lactic acid assay @@ -97660,10 +108693,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hydrogencarbonate assay - An analyte assay that measures the abundance of hydrogencarbonate - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hydrogencarbonate + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hydrogencarbonate assay @@ -97704,10 +108737,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 vancomycin assay - An analyte assay that measures the abundance of vancomycin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of vancomycin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 vancomycin assay @@ -97748,10 +108781,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 tobramycin assay - An analyte assay that measures the abundance of tobramycin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of tobramycin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 tobramycin assay @@ -97792,10 +108825,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 3,3',5'-triiodothyronine assay - An analyte assay that measures the abundance of 3,3',5'-triiodothyronine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of 3,3',5'-triiodothyronine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 3,3',5'-triiodothyronine assay @@ -97836,10 +108869,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 C-reactive protein assay - An analyte assay that measures the abundance of C-reactive protein - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of C-reactive protein + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 C-reactive protein assay @@ -97862,10 +108895,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 megakaryocyte count assay - A cytometry assay that measures the count of megakaryocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of megakaryocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 megakaryocyte count assay @@ -97888,10 +108921,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 mesothelial cell count assay - A cytometry assay that measures the count of mesothelial cells - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of mesothelial cells + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 mesothelial cell count assay @@ -97914,10 +108947,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 macrophage count assay - A cytometry assay that measures the count of macrophages - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of macrophages + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 macrophage count assay @@ -97958,10 +108991,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 3-hydroxybutyric acid assay - An analyte assay that measures the abundance of 3-hydroxybutyric acid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of 3-hydroxybutyric acid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 3-hydroxybutyric acid assay @@ -98031,10 +109064,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 panel5 venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 panel5 venous blood carbon dioxide assay @@ -98104,10 +109137,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 panel5 venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 panel5 venous blood sodium assay @@ -98177,10 +109210,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 panel5 venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 panel5 venous blood creatinine assay @@ -98250,10 +109283,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 panel5 venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 panel5 venous blood potassium assay @@ -98310,10 +109343,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 automated differential venous blood basophil count assay - A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 automated differential venous blood basophil count assay @@ -98370,10 +109403,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 automated differential venous blood neutrophil count assay - A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 automated differential venous blood neutrophil count assay @@ -98430,10 +109463,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 automated differential venous blood eosinophil count assay - A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 automated differential venous blood eosinophil count assay @@ -98490,10 +109523,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 automated differential venous blood lymphocyte count assay - A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 automated differential venous blood lymphocyte count assay @@ -98550,10 +109583,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 automated differential venous blood monocyte count assay - A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 automated differential venous blood monocyte count assay @@ -98623,10 +109656,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood chloride assay - An analyte assay that measures the abundance of chloride in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood chloride assay @@ -98683,10 +109716,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with automated differential venous blood RBC count assay - A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with automated differential venous blood RBC count assay @@ -98743,10 +109776,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with automated differential venous blood platelet count assay - A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with automated differential venous blood platelet count assay @@ -98803,10 +109836,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with automated differential venous blood WBC count assay - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with automated differential venous blood WBC count assay @@ -98863,10 +109896,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with automated differential venous blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with automated differential venous blood hematocrit assay @@ -98936,10 +109969,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with automated differential venous blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with automated differential venous blood hemoglobin assay @@ -99009,10 +110042,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood phosphate assay - An analyte assay that measures the abundance of phosphate in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of phosphate in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood phosphate assay @@ -99082,10 +110115,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver injury venous blood alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver injury venous blood alanine aminotransferase assay @@ -99155,10 +110188,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver injury venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver injury venous blood human alkaline phosphatase assay @@ -99228,10 +110261,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver injury venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver injury venous blood bilirubin assay @@ -99301,10 +110334,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver injury venous blood human aspartate aminotransferase assay - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver injury venous blood human aspartate aminotransferase assay @@ -99374,10 +110407,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood glucose assay @@ -99447,10 +110480,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood magnesium assay - An analyte assay that measures the abundance of magnesium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of magnesium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood magnesium assay @@ -99507,10 +110540,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC venous blood RBC count assay - A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC venous blood RBC count assay @@ -99567,10 +110600,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC venous blood WBC count assay - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC venous blood WBC count assay @@ -99627,10 +110660,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC venous blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC venous blood hematocrit assay @@ -99687,10 +110720,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC venous blood platelet count assay - A cytometry assay that measures the count of platelets in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of platelets in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC venous blood platelet count assay @@ -99760,10 +110793,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC venous blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC venous blood hemoglobin assay @@ -99820,10 +110853,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 corrected venous blood leukocyte count assay - A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 corrected venous blood leukocyte count assay @@ -99893,10 +110926,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood bilirubin assay @@ -99966,10 +110999,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood globulin assay - An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood globulin assay @@ -100039,10 +111072,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood albumin assay @@ -100112,10 +111145,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood human aspartate aminotransferase assay - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood human aspartate aminotransferase assay @@ -100185,10 +111218,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood alanine aminotransferase assay @@ -100258,10 +111291,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood human alkaline phosphatase assay @@ -100331,10 +111364,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver evaluation venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver evaluation venous blood protein assay @@ -100404,10 +111437,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood chloride assay - An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood chloride assay @@ -100477,10 +111510,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood potassium assay @@ -100550,10 +111583,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood sodium assay @@ -100623,10 +111656,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood creatinine assay @@ -100696,10 +111729,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood glucose assay @@ -100770,10 +111803,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood calcium assay @@ -100843,10 +111876,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 basic metabolic panel venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 basic metabolic panel venous blood carbon dioxide assay @@ -100916,10 +111949,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood creatine kinase assay - An analyte assay that measures the abundance of creatine kinase in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatine kinase in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood creatine kinase assay @@ -100990,10 +112023,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood calcium assay @@ -101050,10 +112083,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood ferritin assay - An assay that measures ferritin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures ferritin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood ferritin assay @@ -101124,10 +112157,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood calcium assay @@ -101197,10 +112230,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood iron assay - An analyte assay that measures the abundance of iron in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of iron in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood iron assay @@ -101257,10 +112290,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood band neutrophil count assay - A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood band neutrophil count assay @@ -101317,10 +112350,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood WBC count assay - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood WBC count assay @@ -101377,10 +112410,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood eosinophil count assay - A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood eosinophil count assay @@ -101437,10 +112470,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood lymphocyte count assay - A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood lymphocyte count assay @@ -101497,10 +112530,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood nucleated RBC count assay - A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood nucleated RBC count assay @@ -101557,10 +112590,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood monocyte count assay - A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood monocyte count assay @@ -101617,10 +112650,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood segmented neutrophil count assay - A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood segmented neutrophil count assay @@ -101677,10 +112710,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood basophil count assay - A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood basophil count assay @@ -101750,10 +112783,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood albumin assay @@ -101823,10 +112856,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cardiac enzymes venous blood creatine kinase assay - An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cardiac enzymes venous blood creatine kinase assay @@ -101896,10 +112929,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood haptoglobin assay - An analyte assay that measures the abundance of haptoglobin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of haptoglobin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood haptoglobin assay @@ -101956,10 +112989,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood lactate dehydrogenase assay - An assay that measures lactate dehydrogenase in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactate dehydrogenase in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood lactate dehydrogenase assay @@ -102029,10 +113062,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood prealbunin assay - An analyte assay that measures the abundance of prealbunin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of prealbunin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood prealbunin assay @@ -102102,10 +113135,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel venous blood triglyceride assay - An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel venous blood triglyceride assay @@ -102175,10 +113208,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel venous blood high density lipoprotein assay - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel venous blood high density lipoprotein assay @@ -102248,10 +113281,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel venous blood cholesterol assay - An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel venous blood cholesterol assay @@ -102321,10 +113354,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel venous blood low density lipoprotein assay - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel venous blood low density lipoprotein assay @@ -102381,10 +113414,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood hemoglobin A1c assay - An assay that measures hemoglobin A1c in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures hemoglobin A1c in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood hemoglobin A1c assay @@ -102454,10 +113487,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood uric acid assay - An analyte assay that measures the abundance of uric acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of uric acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood uric acid assay @@ -102527,10 +113560,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood protein assay @@ -102600,10 +113633,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood thyroid stimulating hormone assay - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood thyroid stimulating hormone assay @@ -102673,10 +113706,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood prostate specific antigen assay - An analyte assay that measures the abundance of prostate specific antigen in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of prostate specific antigen in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood prostate specific antigen assay @@ -102733,10 +113766,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 24 hour total urine volume assay - An assay that measures volume in urine as part of a 24 hour total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures volume in urine as part of a 24 hour total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 24 hour total urine volume assay @@ -102806,10 +113839,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 T4 uptake venous blood T4 assay - An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 T4 uptake venous blood T4 assay @@ -102879,10 +113912,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood glucose assay - An analyte assay that measures the abundance of glucose in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood glucose assay @@ -102939,10 +113972,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood cell count assay - A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood cell count assay @@ -103012,10 +114045,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hemoglobin oxygen saturation arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hemoglobin oxygen saturation arterial blood oxygen assay @@ -103085,10 +114118,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hemoglobin oxygen saturation arterial blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hemoglobin oxygen saturation arterial blood hemoglobin assay @@ -103158,10 +114191,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 inpatient profile venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 inpatient profile venous blood sodium assay @@ -103231,10 +114264,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 inpatient profile venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 inpatient profile venous blood creatinine assay @@ -103304,10 +114337,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 inpatient profile venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 inpatient profile venous blood potassium assay @@ -103377,10 +114410,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 inpatient profile venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 inpatient profile venous blood carbon dioxide assay @@ -103450,10 +114483,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood folic acid assay - An analyte assay that measures the abundance of folic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of folic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood folic acid assay @@ -103510,10 +114543,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 count venous blood reticulocyte count assay - A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 count venous blood reticulocyte count assay @@ -103583,10 +114616,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood potassium assay @@ -103656,10 +114689,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood carbon dioxide assay @@ -103729,10 +114762,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood transferrin assay - An analyte assay that measures the abundance of transferrin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of transferrin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood transferrin assay @@ -103802,10 +114835,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood sodium assay @@ -103876,10 +114909,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 random electrolytes urine sodium assay - An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 random electrolytes urine sodium assay @@ -103950,10 +114983,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 random electrolytes urine potassium assay - An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 random electrolytes urine potassium assay @@ -104024,10 +115057,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 urine creatinine assay - An analyte assay that measures the abundance of creatinine in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 urine creatinine assay @@ -104085,10 +115118,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 urine osmolality assay - An assay that measures osmolality in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures osmolality in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 urine osmolality assay @@ -104158,10 +115191,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cooximitery arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cooximitery arterial blood oxygen assay @@ -104231,10 +115264,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cooximitery arterial blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cooximitery arterial blood hemoglobin assay @@ -104304,10 +115337,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cooximitery arterial blood methemoglobin assay - An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cooximitery arterial blood methemoglobin assay @@ -104378,10 +115411,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 electrolytes urine sodium assay - An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 electrolytes urine sodium assay @@ -104452,10 +115485,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 electrolytes urine potassium assay - An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 electrolytes urine potassium assay @@ -104512,10 +115545,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 Biosite cardiac panel arterial blood creatine kinase MB assay - An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 Biosite cardiac panel arterial blood creatine kinase MB assay @@ -104572,10 +115605,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood fibrinogen assay - An assay that measures fibrinogen in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures fibrinogen in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood fibrinogen assay @@ -104645,10 +115678,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood carbon dioxide assay @@ -104719,10 +115752,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood calcium assay @@ -104792,10 +115825,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood potassium assay @@ -104865,10 +115898,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood sodium assay @@ -104938,10 +115971,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood glucose assay @@ -105011,10 +116044,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood albumin assay @@ -105084,10 +116117,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood human alkaline phosphatase assay @@ -105157,10 +116190,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood bilirubin assay @@ -105230,10 +116263,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood chloride assay - An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood chloride assay @@ -105303,10 +116336,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood human aspartate aminotransferase assay - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood human aspartate aminotransferase assay @@ -105376,10 +116409,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood protein assay @@ -105449,10 +116482,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood creatinine assay @@ -105522,10 +116555,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 comprehensive metabolic panel venous blood alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 comprehensive metabolic panel venous blood alanine aminotransferase assay @@ -105582,10 +116615,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood LDH assay - An assay that measures LDH in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures LDH in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood LDH assay @@ -105642,10 +116675,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood creatine kinase MB assay - An assay that measures creatine kinase MB in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures creatine kinase MB in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood creatine kinase MB assay @@ -105702,10 +116735,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood lactic acid assay - An assay that measures lactic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood lactic acid assay @@ -105762,10 +116795,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood hematocrit assay @@ -105835,10 +116868,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood creatinine assay @@ -105908,10 +116941,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 blood gas venous blood oxygen assay - An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 blood gas venous blood oxygen assay @@ -105982,10 +117015,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ionized venous blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ionized venous blood ionized calcium assay @@ -106055,10 +117088,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 blood gas venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 blood gas venous blood carbon dioxide assay @@ -106128,10 +117161,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 blood gas venous blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 blood gas venous blood bicarbonate assay @@ -106201,10 +117234,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood creatinine assay - An analyte assay that measures the abundance of creatinine in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood creatinine assay @@ -106274,10 +117307,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood tacrolimus assay - An analyte assay that measures the abundance of tacrolimus in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of tacrolimus in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood tacrolimus assay @@ -106347,10 +117380,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 random venous blood vancomycin assay - An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 random venous blood vancomycin assay @@ -106420,10 +117453,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood mycophenolic acid assay - An analyte assay that measures the abundance of mycophenolic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of mycophenolic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood mycophenolic acid assay @@ -106493,10 +117526,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 non-vented blood gas arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 non-vented blood gas arterial blood carbon dioxide assay @@ -106566,10 +117599,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 non-vented blood gas arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 non-vented blood gas arterial blood oxygen assay @@ -106639,10 +117672,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 non-vented blood gas arterial blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 non-vented blood gas arterial blood bicarbonate assay @@ -106699,10 +117732,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 quantitative venous blood IgG assay - An assay that measures IgG in venous blood as part of a quantitative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures IgG in venous blood as part of a quantitative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 quantitative venous blood IgG assay @@ -106759,10 +117792,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 quantitative venous blood IgM assay - An assay that measures IgM in venous blood as part of a quantitative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures IgM in venous blood as part of a quantitative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 quantitative venous blood IgM assay @@ -106819,10 +117852,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 quantitative venous blood IgA assay - An assay that measures IgA in venous blood as part of a quantitative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures IgA in venous blood as part of a quantitative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 quantitative venous blood IgA assay @@ -106892,10 +117925,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood sodium assay - An analyte assay that measures the abundance of sodium in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood sodium assay @@ -106965,10 +117998,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood potassium assay - An analyte assay that measures the abundance of potassium in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood potassium assay @@ -107039,10 +118072,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ionized arterial blood calcium assay - An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ionized arterial blood calcium assay @@ -107112,10 +118145,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 vented blood gas arterial blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 vented blood gas arterial blood bicarbonate assay @@ -107185,10 +118218,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 vented blood gas arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 vented blood gas arterial blood oxygen assay @@ -107258,10 +118291,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 vented blood gas arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 vented blood gas arterial blood carbon dioxide assay @@ -107318,10 +118351,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood hematocrit assay @@ -107391,10 +118424,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood chloride assay - An analyte assay that measures the abundance of chloride in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood chloride assay @@ -107464,10 +118497,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood hemoglobin assay @@ -107524,10 +118557,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood hematocrit assay @@ -107598,10 +118631,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood ionized calcium assay @@ -107671,10 +118704,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood potassium assay @@ -107744,10 +118777,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood oxygen assay - An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood oxygen assay @@ -107817,10 +118850,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood hemoglobin assay @@ -107890,10 +118923,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood bicarbonate assay @@ -107963,10 +118996,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood glucose assay @@ -108036,10 +119069,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood sodium assay @@ -108096,10 +119129,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood lactic acid assay - An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood lactic acid assay @@ -108169,10 +119202,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM premier blood gas venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM premier blood gas venous blood carbon dioxide assay @@ -108242,10 +119275,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 trough venous blood tobramycin assay - An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 trough venous blood tobramycin assay @@ -108315,10 +119348,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 random venous blood tobramycin assay - An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 random venous blood tobramycin assay @@ -108375,10 +119408,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood metamyelocyte count assay - A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood metamyelocyte count assay @@ -108435,10 +119468,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 arterial blood lactic acid assay - An assay that measures lactic acid in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactic acid in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 arterial blood lactic acid assay @@ -108508,10 +119541,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood 25-hydroxyvitamin D2 assay - An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood 25-hydroxyvitamin D2 assay @@ -108581,10 +119614,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood digoxin assay - An analyte assay that measures the abundance of digoxin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of digoxin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood digoxin assay @@ -108655,10 +119688,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 urine protein assay - An analyte assay that measures the abundance of protein in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 urine protein assay @@ -108728,10 +119761,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood tobramycin assay - An analyte assay that measures the abundance of tobramycin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of tobramycin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood tobramycin assay @@ -108740,7 +119773,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -108788,10 +119821,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood myelocyte count assay - A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood myelocyte count assay @@ -108861,10 +119894,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 SPEP protein electrophoresis venous blood beta-globin assay - An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 SPEP protein electrophoresis venous blood beta-globin assay @@ -108934,10 +119967,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 SPEP protein electrophoresis venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 SPEP protein electrophoresis venous blood albumin assay @@ -109007,10 +120040,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 SPEP protein electrophoresis venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 SPEP protein electrophoresis venous blood protein assay @@ -109080,10 +120113,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 trough venous blood vancomycin assay - An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 trough venous blood vancomycin assay @@ -109153,10 +120186,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hepatic panel venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hepatic panel venous blood protein assay @@ -109226,10 +120259,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hepatic panel venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hepatic panel venous blood bilirubin assay @@ -109299,10 +120332,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hepatic panel venous blood alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hepatic panel venous blood alanine aminotransferase assay @@ -109372,10 +120405,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hepatic panel venous blood human aspartate aminotransferase assay - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hepatic panel venous blood human aspartate aminotransferase assay @@ -109445,10 +120478,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hepatic panel venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hepatic panel venous blood albumin assay @@ -109518,10 +120551,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hepatic panel venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hepatic panel venous blood human alkaline phosphatase assay @@ -109578,10 +120611,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 estimated venous blood glomerular filtration assay - An assay that measures glomerular filtration in venous blood as part of a estimated order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures glomerular filtration in venous blood as part of a estimated order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 estimated venous blood glomerular filtration assay @@ -109651,10 +120684,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 DT60 venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 DT60 venous blood creatinine assay @@ -109724,10 +120757,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 fasting venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 fasting venous blood glucose assay @@ -109797,10 +120830,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 random venous blood amikacin assay - An analyte assay that measures the abundance of amikacin in venous blood as part of a random order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of amikacin in venous blood as part of a random order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 random venous blood amikacin assay @@ -109870,10 +120903,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood ammonia assay - An analyte assay that measures the abundance of ammonia in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ammonia in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood ammonia assay @@ -109943,10 +120976,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood GGT assay - An analyte assay that measures the abundance of GGT in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of GGT in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood GGT assay @@ -110016,10 +121049,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood phosphate assay - An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood phosphate assay @@ -110089,10 +121122,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood potassium assay @@ -110163,10 +121196,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood calcium assay @@ -110236,10 +121269,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood glucose assay @@ -110309,10 +121342,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood carbon dioxide assay @@ -110382,10 +121415,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood albumin assay @@ -110455,10 +121488,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood sodium assay @@ -110528,10 +121561,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood magnesium assay - An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood magnesium assay @@ -110601,10 +121634,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood creatinine assay @@ -110674,10 +121707,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem11 venous blood chloride assay - An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem11 venous blood chloride assay @@ -110734,10 +121767,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood IgE assay - An assay that measures IgE in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures IgE in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood IgE assay @@ -110807,10 +121840,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood human aspartate aminotransferase assay - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood human aspartate aminotransferase assay @@ -110880,10 +121913,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood creatinine assay - An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood creatinine assay @@ -110953,10 +121986,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood magnesium assay - An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood magnesium assay @@ -111026,10 +122059,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood carbon dioxide assay @@ -111099,10 +122132,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood glucose assay @@ -111173,10 +122206,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood calcium assay @@ -111246,10 +122279,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood triglyceride assay - An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood triglyceride assay @@ -111319,10 +122352,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood sodium assay @@ -111392,10 +122425,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood phosphate assay - An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood phosphate assay @@ -111465,10 +122498,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood human alkaline phosphatase assay @@ -111538,10 +122571,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood albumin assay @@ -111611,10 +122644,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood bilirubin assay @@ -111684,10 +122717,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood chloride assay - An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood chloride assay @@ -111757,10 +122790,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood alanine aminotransferase assay @@ -111830,10 +122863,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chem16 venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 chem16 venous blood potassium assay @@ -111903,10 +122936,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood glucose assay - An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood glucose assay @@ -111977,10 +123010,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood ionized calcium assay @@ -112050,10 +123083,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood potassium assay - An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood potassium assay @@ -112123,10 +123156,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood sodium assay - An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood sodium assay @@ -112196,10 +123229,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood creatinine assay - An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood creatinine assay @@ -112256,10 +123289,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood hematocrit assay @@ -112329,10 +123362,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC chem8 arterial blood chloride assay - An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC chem8 arterial blood chloride assay @@ -112402,10 +123435,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 peak venous blood tobramycin assay - An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 peak venous blood tobramycin assay @@ -112476,10 +123509,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 24 hour urine creatinine assay - An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 24 hour urine creatinine assay @@ -112549,10 +123582,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 intact venous blood PTH assay - An analyte assay that measures the abundance of PTH in venous blood as part of a intact order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of PTH in venous blood as part of a intact order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 intact venous blood PTH assay @@ -112622,10 +123655,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood PSA assay - An analyte assay that measures the abundance of PSA in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of PSA in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood PSA assay @@ -112695,10 +123728,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood T3 assay - An analyte assay that measures the abundance of T3 in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of T3 in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood T3 assay @@ -112769,10 +123802,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 24 hour urine protein assay - An analyte assay that measures the abundance of protein in urine as part of a 24 hour order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in urine as part of a 24 hour order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 24 hour urine protein assay @@ -112842,10 +123875,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood cholesterol assay - An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood cholesterol assay @@ -112915,10 +123948,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood triglyceride assay - An analyte assay that measures the abundance of triglyceride in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of triglyceride in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood triglyceride assay @@ -112975,10 +124008,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 tube 4 count cerebrospinal fluid cell count assay - A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 tube 4 count cerebrospinal fluid cell count assay @@ -113048,10 +124081,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid protein assay - An analyte assay that measures the abundance of protein in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid protein assay @@ -113121,10 +124154,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid glucose assay - An analyte assay that measures the abundance of glucose in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid glucose assay @@ -113181,10 +124214,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 tube 1 count cerebrospinal fluid cell count assay - A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 tube 1 count cerebrospinal fluid cell count assay @@ -113254,10 +124287,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood dehydroepiandrosterone assay - An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood dehydroepiandrosterone assay @@ -113327,10 +124360,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood cortisol assay - An analyte assay that measures the abundance of cortisol in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of cortisol in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood cortisol assay @@ -113400,10 +124433,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood sodium assay - An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood sodium assay @@ -113473,10 +124506,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood oxygen assay @@ -113546,10 +124579,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood glucose assay - An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood glucose assay @@ -113606,10 +124639,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood lactic acid assay - An assay that measures lactic acid in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactic acid in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood lactic acid assay @@ -113679,10 +124712,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood hemoglobin assay @@ -113752,10 +124785,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood chloride assay - An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood chloride assay @@ -113825,10 +124858,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood carbon dioxide assay @@ -113885,10 +124918,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood hematocrit assay @@ -113959,10 +124992,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood calcium assay - An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood calcium assay @@ -114019,10 +125052,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood temperature assay - An assay that measures temperature in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures temperature in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood temperature assay @@ -114092,10 +125125,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood bicarbonate assay @@ -114165,10 +125198,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood potassium assay - An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood potassium assay @@ -114225,10 +125258,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood promyelocyte count assay - A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood promyelocyte count assay @@ -114298,10 +125331,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood glucose assay - An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood glucose assay @@ -114371,10 +125404,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood hemoglobin assay @@ -114445,10 +125478,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood ionized calcium assay @@ -114518,10 +125551,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood carbon dioxide assay @@ -114578,10 +125611,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood hematocrit assay @@ -114651,10 +125684,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood sodium assay - An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood sodium assay @@ -114724,10 +125757,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood oxygen assay - An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood oxygen assay @@ -114797,10 +125830,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood bicarbonate assay @@ -114857,10 +125890,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood lactic acid assay - An assay that measures lactic acid in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactic acid in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood lactic acid assay @@ -114930,10 +125963,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood chloride assay - An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood chloride assay @@ -115003,10 +126036,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood T4 assay - An analyte assay that measures the abundance of T4 in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of T4 in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood T4 assay @@ -115076,10 +126109,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 free venous blood T4 assay - An analyte assay that measures the abundance of T4 in venous blood as part of a free order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of T4 in venous blood as part of a free order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 free venous blood T4 assay @@ -115149,10 +126182,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood potassium assay - An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood potassium assay @@ -115223,10 +126256,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 urine sodium assay - An analyte assay that measures the abundance of sodium in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 urine sodium assay @@ -115296,10 +126329,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bone profile venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bone profile venous blood albumin assay @@ -115370,10 +126403,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bone profile venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bone profile venous blood calcium assay @@ -115443,10 +126476,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bone profile venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bone profile venous blood human alkaline phosphatase assay @@ -115516,10 +126549,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bone profile venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bone profile venous blood protein assay @@ -115589,10 +126622,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bone profile venous blood phosphate assay - An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bone profile venous blood phosphate assay @@ -115662,10 +126695,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABG/electrolytes arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABG/electrolytes arterial blood carbon dioxide assay @@ -115735,10 +126768,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABG/electrolytes arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABG/electrolytes arterial blood oxygen assay @@ -115809,10 +126842,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABG/electrolytes arterial blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABG/electrolytes arterial blood ionized calcium assay @@ -115869,10 +126902,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with automated differential venous blood nucleated RBC count assay - A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with automated differential venous blood nucleated RBC count assay @@ -115942,10 +126975,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel venous blood methemoglobin assay - An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel venous blood methemoglobin assay @@ -116015,10 +127048,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ABL90 panel arterial blood methemoglobin assay - An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ABL90 panel arterial blood methemoglobin assay @@ -116088,10 +127121,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood valproic acid assay - An analyte assay that measures the abundance of valproic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of valproic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood valproic acid assay @@ -116161,10 +127194,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 high sensitivity cardiac/neonatal venous blood c-reactive protein assay - An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 high sensitivity cardiac/neonatal venous blood c-reactive protein assay @@ -116234,10 +127267,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 POC arterial blood creatinine assay - An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 POC arterial blood creatinine assay @@ -116307,10 +127340,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood bicarbonate assay @@ -116380,10 +127413,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood oxygen assay @@ -116440,10 +127473,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood hematocrit assay @@ -116500,10 +127533,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood temperature assay - An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood temperature assay @@ -116573,10 +127606,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood hemoglobin assay @@ -116646,10 +127679,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood potassium assay - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood potassium assay @@ -116719,10 +127752,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood glucose assay - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood glucose assay @@ -116793,10 +127826,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood ionized calcium assay @@ -116866,10 +127899,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood carbon dioxide assay @@ -116939,10 +127972,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4000 ANLCOOX arterial blood sodium assay - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4000 ANLCOOX arterial blood sodium assay @@ -117013,10 +128046,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 ionized venous blood calcium assay - An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 ionized venous blood calcium assay @@ -117086,10 +128119,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood hemoglobin assay @@ -117146,10 +128179,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood megakaryocyte count assay - A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood megakaryocyte count assay @@ -117219,10 +128252,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 non-cardiac venous blood c-reactive protein assay - An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 non-cardiac venous blood c-reactive protein assay @@ -117292,10 +128325,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 intraoperative venous blood PTH assay - An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 intraoperative venous blood PTH assay @@ -117365,10 +128398,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood parathyroid hormone assay - An analyte assay that measures the abundance of parathyroid hormone in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of parathyroid hormone in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood parathyroid hormone assay @@ -117438,10 +128471,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total bodily fluid protein assay - An analyte assay that measures the abundance of protein in bodily fluid as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in bodily fluid as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total bodily fluid protein assay @@ -117511,10 +128544,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bodily fluid glucose assay - An analyte assay that measures the abundance of glucose in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bodily fluid glucose assay @@ -117571,10 +128604,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 count bodily fluid cell count assay - A cytometry assay that measures the count of cells in bodily fluid as part of a count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of cells in bodily fluid as part of a count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 count bodily fluid cell count assay @@ -117631,10 +128664,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid segmented neutrophil count assay - A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid segmented neutrophil count assay @@ -117691,10 +128724,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid mesothelial cell count assay - A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid mesothelial cell count assay @@ -117751,10 +128784,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid monocyte count assay - A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid monocyte count assay @@ -117811,10 +128844,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid lymphocyte count assay - A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid lymphocyte count assay @@ -117871,10 +128904,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid macrophage count assay - A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid macrophage count assay @@ -117931,10 +128964,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid basophil count assay - A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid basophil count assay @@ -117991,10 +129024,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 manual differential bodily fluid eosinophil count assay - A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 manual differential bodily fluid eosinophil count assay @@ -118064,10 +129097,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver function venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver function venous blood bilirubin assay @@ -118137,10 +129170,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver function venous blood alanine aminotransferase assay - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver function venous blood alanine aminotransferase assay @@ -118210,10 +129243,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver function venous blood human aspartate aminotransferase assay - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver function venous blood human aspartate aminotransferase assay @@ -118283,10 +129316,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver function venous blood albumin assay - An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver function venous blood albumin assay @@ -118356,10 +129389,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver function venous blood protein assay - An analyte assay that measures the abundance of protein in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of protein in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver function venous blood protein assay @@ -118429,10 +129462,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver function venous blood human alkaline phosphatase assay - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver function venous blood human alkaline phosphatase assay @@ -118502,10 +129535,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 vitamin B12 and Folate venous blood folic acid assay - An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 vitamin B12 and Folate venous blood folic acid assay @@ -118562,10 +129595,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bodily fluid cell count assay - A cytometry assay that measures the count of cells in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of cells in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bodily fluid cell count assay @@ -118622,10 +129655,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood reticulocyte count assay - A cytometry assay that measures the count of reticulocytes in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of reticulocytes in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood reticulocyte count assay @@ -118695,10 +129728,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bodily fluid cholesterol assay - An analyte assay that measures the abundance of cholesterol in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of cholesterol in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bodily fluid cholesterol assay @@ -118768,10 +129801,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 TSH reflex Free T4 venous blood thyroid stimulating hormone assay - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 TSH reflex Free T4 venous blood thyroid stimulating hormone assay @@ -118841,10 +129874,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 direct venous blood bilirubin assay - An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 direct venous blood bilirubin assay @@ -118914,10 +129947,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 free venous blood T3 assay - An analyte assay that measures the abundance of T3 in venous blood as part of a free order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of T3 in venous blood as part of a free order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 free venous blood T3 assay @@ -118987,10 +130020,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bodily fluid albumin assay - An analyte assay that measures the abundance of albumin in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of albumin in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bodily fluid albumin assay @@ -119060,10 +130093,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 bodily fluid triglyceride assay - An analyte assay that measures the abundance of triglyceride in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of triglyceride in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 bodily fluid triglyceride assay @@ -119120,10 +130153,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hemoglobin and hematocrit venous blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hemoglobin and hematocrit venous blood hematocrit assay @@ -119193,10 +130226,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 hemoglobin and hematocrit venous blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 hemoglobin and hematocrit venous blood hemoglobin assay @@ -119267,10 +130300,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood ionized calcium assay @@ -119327,10 +130360,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood temperature assay - An assay that measures temperature in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures temperature in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood temperature assay @@ -119400,10 +130433,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood bicarbonate assay @@ -119473,10 +130506,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood oxygen assay - An analyte assay that measures the abundance of oxygen in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood oxygen assay @@ -119533,10 +130566,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood osmolality assay - An assay that measures osmolality in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures osmolality in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood osmolality assay @@ -119593,10 +130626,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver fibrosis (chronic viral hepatitis) venous blood platelet count assay - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver fibrosis (chronic viral hepatitis) venous blood platelet count assay @@ -119666,10 +130699,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood T3 assay - An analyte assay that measures the abundance of T3 in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of T3 in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood T3 assay @@ -119726,10 +130759,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood neutrophil count assay - A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood neutrophil count assay @@ -119800,10 +130833,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 creatinine clearance urine creatinine assay - An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 creatinine clearance urine creatinine assay @@ -119873,10 +130906,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood beta hydroxybutryic acid assay - An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood beta hydroxybutryic acid assay @@ -119933,10 +130966,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood megakaryocyte count assay - A cytometry assay that measures the count of megakaryocytes in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of megakaryocytes in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood megakaryocyte count assay @@ -119993,10 +131026,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood nucleated RBC count assay - A cytometry assay that measures the count of nucleated RBCs in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of nucleated RBCs in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood nucleated RBC count assay @@ -120053,10 +131086,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood WBC count assay - A cytometry assay that measures the count of WBCs in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of WBCs in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood WBC count assay @@ -120113,10 +131146,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 automated count venous blood reticulocyte count assay - A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 automated count venous blood reticulocyte count assay @@ -120186,10 +131219,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 total venous blood homocysteine assay - An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 total venous blood homocysteine assay @@ -120259,10 +131292,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood Ceruloplasmin assay - An analyte assay that measures the abundance of Ceruloplasmin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of Ceruloplasmin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood Ceruloplasmin assay @@ -120332,10 +131365,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood bicarbonate assay @@ -120392,10 +131425,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood lactic acid assay - An assay that measures lactic acid in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures lactic acid in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood lactic acid assay @@ -120465,10 +131498,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood hemoglobin assay - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood hemoglobin assay @@ -120538,10 +131571,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood sodium assay - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood sodium assay @@ -120611,10 +131644,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood potassium assay - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood potassium assay @@ -120671,10 +131704,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood temperature assay - An assay that measures temperature in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An assay that measures temperature in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood temperature assay @@ -120744,10 +131777,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood glucose assay - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood glucose assay @@ -120817,10 +131850,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood oxygen assay @@ -120877,10 +131910,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood hematocrit assay - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood hematocrit assay @@ -120951,10 +131984,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood ionized calcium assay - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood ionized calcium assay @@ -121024,10 +132057,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 GEM4 arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 GEM4 arterial blood carbon dioxide assay @@ -121084,10 +132117,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 liver fibrosis (NAFLD) venous blood platelet count assay - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 liver fibrosis (NAFLD) venous blood platelet count assay @@ -121157,10 +132190,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood beta hydroxybutric acid assay - An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood beta hydroxybutric acid assay @@ -121217,10 +132250,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 CBC with manual differential venous blood plasma cell count assay - A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 CBC with manual differential venous blood plasma cell count assay @@ -121290,10 +132323,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood erythropoietin assay - An analyte assay that measures the abundance of erythropoietin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of erythropoietin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood erythropoietin assay @@ -121363,10 +132396,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 blood gas arterial blood oxygen assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 blood gas arterial blood oxygen assay @@ -121436,10 +132469,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 blood gas arterial blood bicarbonate assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 blood gas arterial blood bicarbonate assay @@ -121509,10 +132542,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 blood gas arterial blood carbon dioxide assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 blood gas arterial blood carbon dioxide assay @@ -121582,10 +132615,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 free/total venous blood PSA assay - An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 free/total venous blood PSA assay @@ -121642,10 +132675,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid lymphocyte count assay - A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid lymphocyte count assay @@ -121702,10 +132735,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid segmented neutrophil count assay - A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid segmented neutrophil count assay @@ -121762,10 +132795,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid mesothelial cell count assay - A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid mesothelial cell count assay @@ -121822,10 +132855,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid macrophage count assay - A cytometry assay that measures the count of macrophages in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of macrophages in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid macrophage count assay @@ -121882,10 +132915,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid basophil count assay - A cytometry assay that measures the count of basophils in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of basophils in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid basophil count assay @@ -121942,10 +132975,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid monocyte count assay - A cytometry assay that measures the count of monocytes in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of monocytes in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid monocyte count assay @@ -122002,10 +133035,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 cerebrospinal fluid eosinophil count assay - A cytometry assay that measures the count of eosinophils in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + A cytometry assay that measures the count of eosinophils in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 cerebrospinal fluid eosinophil count assay @@ -122075,10 +133108,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 venous blood beta-2-microglobulin assay - An analyte assay that measures the abundance of beta-2-microglobulin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of beta-2-microglobulin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 venous blood beta-2-microglobulin assay @@ -122148,10 +133181,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel reflex direct venous blood low density lipoprotein assay - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel reflex direct venous blood low density lipoprotein assay @@ -122221,10 +133254,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel reflex direct venous blood triglyceride assay - An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel reflex direct venous blood triglyceride assay @@ -122294,10 +133327,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel reflex direct venous blood cholesterol assay - An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel reflex direct venous blood cholesterol assay @@ -122367,10 +133400,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 lipid panel reflex direct venous blood high density lipoprotein assay - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 lipid panel reflex direct venous blood high density lipoprotein assay @@ -122445,13 +133478,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 pooled clone sequencing assay - Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. + Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. - A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. - Dan Berrios, ORCID: 0000-0003-4312-9552 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ - https://github.com/obi-ontology/obi/issues/1106 - Bonita Lam + A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. + Dan Berrios, ORCID: 0000-0003-4312-9552 + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ + https://github.com/obi-ontology/obi/issues/1106 + Bonita Lam pooled clone sequencing assay @@ -122492,11 +133525,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 chromium release assay - Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. + Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. - IEDB - PlanAndPlannedProcess Branch + An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. + IEDB + PlanAndPlannedProcess Branch chromium release assay @@ -122550,7 +133583,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 disease course The totality of all processes through which a given disease instance is realized. - replace 'OBI:occurrence of disease', need to add logical definition + replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease @@ -122631,10 +133664,10 @@ realizes some 'host of immune response role' - parasite organism - An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. + parasite organism + An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. - parasite organism + parasite organism @@ -122643,10 +133676,10 @@ realizes some 'host of immune response role' - Plasmodium gametocyte - A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes + Plasmodium gametocyte + A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes - Plasmodium gametocyte + Plasmodium gametocyte @@ -122655,10 +133688,10 @@ realizes some 'host of immune response role' - age - A time quality inhering in a bearer by virtue of how long the bearer has existed. + age + A time quality inhering in a bearer by virtue of how long the bearer has existed. - age + age @@ -122667,10 +133700,10 @@ realizes some 'host of immune response role' - fluorescence - A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. + fluorescence + A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. - fluorescence + fluorescence @@ -122679,10 +133712,10 @@ realizes some 'host of immune response role' - composition - A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. + composition + A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. - composition + composition @@ -122691,10 +133724,10 @@ realizes some 'host of immune response role' - concentration of - A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. + concentration of + A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. - concentration of + concentration of @@ -122703,10 +133736,10 @@ realizes some 'host of immune response role' - biological sex - An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + biological sex + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. - biological sex + biological sex @@ -122715,10 +133748,10 @@ realizes some 'host of immune response role' - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + morphology + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - morphology + morphology @@ -122727,10 +133760,10 @@ realizes some 'host of immune response role' - size - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + size + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. - size + size @@ -122739,10 +133772,10 @@ realizes some 'host of immune response role' - length - A 1-D extent quality which is equal to the distance between two points. + length + A 1-D extent quality which is equal to the distance between two points. - length + length @@ -122751,10 +133784,10 @@ realizes some 'host of immune response role' - mass - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. + mass + A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - mass + mass @@ -122763,10 +133796,10 @@ realizes some 'host of immune response role' - position - A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. + position + A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. - position + position @@ -122775,10 +133808,10 @@ realizes some 'host of immune response role' - structure - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. + structure + A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - structure + structure @@ -122787,10 +133820,10 @@ realizes some 'host of immune response role' - temperature - A physical quality of the thermal energy of a system. + temperature + A physical quality of the thermal energy of a system. - temperature + temperature @@ -122799,10 +133832,10 @@ realizes some 'host of immune response role' - time - A quality in which events occur in sequence. + time + A quality in which events occur in sequence. - time + time @@ -122811,10 +133844,10 @@ realizes some 'host of immune response role' - viability - An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. + viability + An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. - viability + viability @@ -122823,10 +133856,10 @@ realizes some 'host of immune response role' - behavioral quality - An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. + behavioral quality + An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. - behavioral quality + behavioral quality @@ -122835,10 +133868,10 @@ realizes some 'host of immune response role' - female - A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + female + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. - female + female @@ -122847,10 +133880,10 @@ realizes some 'host of immune response role' - male - A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + male + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. - male + male @@ -122859,10 +133892,10 @@ realizes some 'host of immune response role' - volume - A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. + volume + A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. - volume + volume @@ -122871,10 +133904,10 @@ realizes some 'host of immune response role' - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + physical quality + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - physical quality + physical quality @@ -122883,10 +133916,10 @@ realizes some 'host of immune response role' - damage - A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. + damage + A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. - damage + damage @@ -122895,10 +133928,10 @@ realizes some 'host of immune response role' - pressure - A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. + pressure + A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. - pressure + pressure @@ -122907,10 +133940,10 @@ realizes some 'host of immune response role' - diluted - A concentration which relatively low. + diluted + A concentration which relatively low. - diluted + diluted @@ -122919,10 +133952,10 @@ realizes some 'host of immune response role' - damaged - A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. + damaged + A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. - damaged + damaged @@ -122931,10 +133964,10 @@ realizes some 'host of immune response role' - lateral to - A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. + lateral to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. - lateral to + lateral to @@ -122943,10 +133976,10 @@ realizes some 'host of immune response role' - ventral to - A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. + ventral to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. - ventral to + ventral to @@ -122955,10 +133988,10 @@ realizes some 'host of immune response role' - dorsal to - A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. + dorsal to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. - dorsal to + dorsal to @@ -122967,10 +134000,10 @@ realizes some 'host of immune response role' - physical object quality - A quality which inheres in a continuant. + physical object quality + A quality which inheres in a continuant. - physical object quality + physical object quality @@ -122979,10 +134012,10 @@ realizes some 'host of immune response role' - electromagnetic (EM) radiation quality - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. + electromagnetic (EM) radiation quality + A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - electromagnetic (EM) radiation quality + electromagnetic (EM) radiation quality @@ -122991,10 +134024,10 @@ realizes some 'host of immune response role' - luminous flux - A scalar optical quality which obtains by the magnitude of the light emitted by the bearer. + luminous flux + A scalar optical quality which obtains by the magnitude of the light emitted by the bearer. - luminous flux + luminous flux @@ -123003,10 +134036,10 @@ realizes some 'host of immune response role' - optical quality - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. + optical quality + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - optical quality + optical quality @@ -123015,10 +134048,10 @@ realizes some 'host of immune response role' - bacterial mating type - A mating type that indicates whether the F plasmid has integrated into the chromosome. + bacterial mating type + A mating type that indicates whether the F plasmid has integrated into the chromosome. - bacterial mating type + bacterial mating type @@ -123027,10 +134060,10 @@ realizes some 'host of immune response role' - yeast mating type - A yeast mating type. + yeast mating type + A yeast mating type. - yeast mating type + yeast mating type @@ -123039,10 +134072,10 @@ realizes some 'host of immune response role' - mixed sex - A biological sex quality inhering in a population of multiple sexes. + mixed sex + A biological sex quality inhering in a population of multiple sexes. - mixed sex + mixed sex @@ -123051,10 +134084,10 @@ realizes some 'host of immune response role' - biomaterial purity - A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. + biomaterial purity + A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. - biomaterial purity + biomaterial purity @@ -123063,10 +134096,10 @@ realizes some 'host of immune response role' - hermaphrodite - A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. + hermaphrodite + A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. - hermaphrodite + hermaphrodite @@ -123075,10 +134108,10 @@ realizes some 'host of immune response role' - a mating type (yeast) - A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. + a mating type (yeast) + A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. - a mating type (yeast) + a mating type (yeast) @@ -123087,10 +134120,10 @@ realizes some 'host of immune response role' - Saccharomyces cerevisiae mating type - A S. cerevisiae mating type. + Saccharomyces cerevisiae mating type + A S. cerevisiae mating type. - Saccharomyces cerevisiae mating type + Saccharomyces cerevisiae mating type @@ -123099,10 +134132,10 @@ realizes some 'host of immune response role' - Schizosaccharomyces pombe mating type - A S. pombe mating type determined by the gene configuration on the mat1 locus. + Schizosaccharomyces pombe mating type + A S. pombe mating type determined by the gene configuration on the mat1 locus. - Schizosaccharomyces pombe mating type + Schizosaccharomyces pombe mating type @@ -123111,10 +134144,10 @@ realizes some 'host of immune response role' - alpha mating type (yeast) - A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. + alpha mating type (yeast) + A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. - alpha mating type (yeast) + alpha mating type (yeast) @@ -123123,10 +134156,10 @@ realizes some 'host of immune response role' - h minus - A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. + h minus + A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. - h minus + h minus @@ -123135,10 +134168,10 @@ realizes some 'host of immune response role' - h plus - A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. + h plus + A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. - h plus + h plus @@ -123147,10 +134180,10 @@ realizes some 'host of immune response role' - F mating type - A bacterial mating type indicating the presence of F plasmid in a bacterial cell. + F mating type + A bacterial mating type indicating the presence of F plasmid in a bacterial cell. - F mating type + F mating type @@ -123159,10 +134192,10 @@ realizes some 'host of immune response role' - F minus mating type - A bacterial mating type indicating the absence of F plasmid in a bacterial cell. + F minus mating type + A bacterial mating type indicating the absence of F plasmid in a bacterial cell. - F minus mating type + F minus mating type @@ -123171,10 +134204,10 @@ realizes some 'host of immune response role' - ploidy - A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. + ploidy + A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. - ploidy + ploidy @@ -123183,10 +134216,10 @@ realizes some 'host of immune response role' - haploid - A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. + haploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. - haploid + haploid @@ -123195,10 +134228,10 @@ realizes some 'host of immune response role' - polyploid - A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. + polyploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. - polyploid + polyploid @@ -123207,10 +134240,10 @@ realizes some 'host of immune response role' - aneuploid - A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. + aneuploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. - aneuploid + aneuploid @@ -123219,10 +134252,10 @@ realizes some 'host of immune response role' - euploid - A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. + euploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. - euploid + euploid @@ -123231,10 +134264,10 @@ realizes some 'host of immune response role' - diploid - A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. + diploid + A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. - diploid + diploid @@ -123243,10 +134276,10 @@ realizes some 'host of immune response role' - cellular quality - A monadic quality of continuant that exists at the cellular level of organisation. + cellular quality + A monadic quality of continuant that exists at the cellular level of organisation. - cellular quality + cellular quality @@ -123255,10 +134288,10 @@ realizes some 'host of immune response role' - alive - A viability quality inhering in a bearer by virtue of the bearer's condition before death. + alive + A viability quality inhering in a bearer by virtue of the bearer's condition before death. - alive + alive @@ -123267,10 +134300,10 @@ realizes some 'host of immune response role' - dead - A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. + dead + A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. - dead + dead @@ -123279,10 +134312,10 @@ realizes some 'host of immune response role' - quality of a solid - A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. + quality of a solid + A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. - quality of a solid + quality of a solid @@ -123291,10 +134324,10 @@ realizes some 'host of immune response role' - quality of a gas - A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. + quality of a gas + A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. - quality of a gas + quality of a gas @@ -123303,10 +134336,10 @@ realizes some 'host of immune response role' - quality of a liquid - A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. + quality of a liquid + A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. - quality of a liquid + quality of a liquid @@ -123315,10 +134348,10 @@ realizes some 'host of immune response role' - flow rate - A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. + flow rate + A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. - flow rate + flow rate @@ -123327,11 +134360,11 @@ realizes some 'host of immune response role' - anterior to - A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. + anterior to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. frontal - anterior to + anterior to @@ -123340,10 +134373,10 @@ realizes some 'host of immune response role' - 3-D extent - A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. + 3-D extent + A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. - 3-D extent + 3-D extent @@ -123352,10 +134385,10 @@ realizes some 'host of immune response role' - radiation quality - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + radiation quality + A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - radiation quality + radiation quality @@ -123364,10 +134397,10 @@ realizes some 'host of immune response role' - activity (of a radionuclide) - A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. + activity (of a radionuclide) + A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. - activity (of a radionuclide) + activity (of a radionuclide) @@ -123376,10 +134409,10 @@ realizes some 'host of immune response role' - radioactive - A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. + radioactive + A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. - radioactive + radioactive @@ -123388,10 +134421,10 @@ realizes some 'host of immune response role' - left side of - A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. + left side of + A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. - left side of + left side of @@ -123400,10 +134433,10 @@ realizes some 'host of immune response role' - right side of - A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. + right side of + A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. - right side of + right side of @@ -123412,10 +134445,10 @@ realizes some 'host of immune response role' - phenotypic sex - An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + phenotypic sex + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. - phenotypic sex + phenotypic sex @@ -123424,10 +134457,10 @@ realizes some 'host of immune response role' - mating type - A biological sex quality inhering in an individual or a population that undergo sexual reproduction. + mating type + A biological sex quality inhering in an individual or a population that undergo sexual reproduction. - mating type + mating type @@ -123436,10 +134469,10 @@ realizes some 'host of immune response role' - movement quality - A physical quality inhering in a bearer by virtue of the bearer's participation in movement. + movement quality + A physical quality inhering in a bearer by virtue of the bearer's participation in movement. - movement quality + movement quality @@ -123448,10 +134481,10 @@ realizes some 'host of immune response role' - frozen - A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. + frozen + A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. - frozen + frozen @@ -123460,10 +134493,10 @@ realizes some 'host of immune response role' - organismal quality - A quality that inheres in an entire organism or part of an organism. + organismal quality + A quality that inheres in an entire organism or part of an organism. - organismal quality + organismal quality @@ -123472,10 +134505,10 @@ realizes some 'host of immune response role' - population quality - A quality that inheres in an entire population or part of a population. + population quality + A quality that inheres in an entire population or part of a population. - population quality + population quality @@ -123484,10 +134517,10 @@ realizes some 'host of immune response role' - osmolality - A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent. + osmolality + A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent. - osmolality + osmolality @@ -123496,10 +134529,10 @@ realizes some 'host of immune response role' - molecular quality - A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. + molecular quality + A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. - molecular quality + molecular quality @@ -123508,10 +134541,10 @@ realizes some 'host of immune response role' - quality of a substance - A quality inhering in a bearer by virtue of its constitution. + quality of a substance + A quality inhering in a bearer by virtue of its constitution. - quality of a substance + quality of a substance @@ -123520,10 +134553,10 @@ realizes some 'host of immune response role' - handedness - A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. + handedness + A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. - handedness + handedness @@ -123532,10 +134565,10 @@ realizes some 'host of immune response role' - left handedness - Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + left handedness + Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. - left handedness + left handedness @@ -123544,10 +134577,10 @@ realizes some 'host of immune response role' - right handedness - Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + right handedness + Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. - right handedness + right handedness @@ -123556,10 +134589,10 @@ realizes some 'host of immune response role' - ambidextrous handedness - Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. + ambidextrous handedness + Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. - ambidextrous handedness + ambidextrous handedness @@ -123568,10 +134601,10 @@ realizes some 'host of immune response role' - fluid flow rate - A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. + fluid flow rate + A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. - fluid flow rate + fluid flow rate @@ -123580,11 +134613,11 @@ realizes some 'host of immune response role' - protein - antithrombin III is a protein - An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. + protein + antithrombin III is a protein + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. - protein + protein @@ -123593,10 +134626,10 @@ realizes some 'host of immune response role' - CD4 molecule - A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. + CD4 molecule + A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. - CD4 molecule + CD4 molecule @@ -123605,10 +134638,10 @@ realizes some 'host of immune response role' - CD3 subunit with immunoglobulin domain - A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. + CD3 subunit with immunoglobulin domain + A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. - CD3 subunit with immunoglobulin domain + CD3 subunit with immunoglobulin domain @@ -123617,10 +134650,10 @@ realizes some 'host of immune response role' - prostate-specific antigen - A protein that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof. + prostate-specific antigen + A protein that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof. - prostate-specific antigen + prostate-specific antigen @@ -123629,10 +134662,10 @@ realizes some 'host of immune response role' - antithrombin-III - A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. + antithrombin-III + A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. - antithrombin-III + antithrombin-III @@ -123641,10 +134674,22 @@ realizes some 'host of immune response role' - double-stranded RNA-specific adenosine deaminase - A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. + double-stranded RNA-specific adenosine deaminase + A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. - double-stranded RNA-specific adenosine deaminase + double-stranded RNA-specific adenosine deaminase + + + + + + + + + adiponectin + A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof. + + adiponectin @@ -123653,10 +134698,10 @@ realizes some 'host of immune response role' - albumin - A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof. + albumin + A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof. - albumin + albumin @@ -123665,10 +134710,10 @@ realizes some 'host of immune response role' - beta-2-microglobulin - A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof. + beta-2-microglobulin + A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof. - beta-2-microglobulin + beta-2-microglobulin @@ -123677,10 +134722,10 @@ realizes some 'host of immune response role' - ceruloplasmin - A protein that is a translation product of the human CP gene or a 1:1 ortholog thereof. + ceruloplasmin + A protein that is a translation product of the human CP gene or a 1:1 ortholog thereof. - ceruloplasmin + ceruloplasmin @@ -123689,10 +134734,10 @@ realizes some 'host of immune response role' - C-reactive protein - A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof. + C-reactive protein + A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof. - C-reactive protein + C-reactive protein @@ -123701,10 +134746,10 @@ realizes some 'host of immune response role' - deoxyribonuclease-1 - A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. + deoxyribonuclease-1 + A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. - deoxyribonuclease-1 + deoxyribonuclease-1 @@ -123713,10 +134758,10 @@ realizes some 'host of immune response role' - erythropoietin - A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof. + erythropoietin + A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof. - erythropoietin + erythropoietin @@ -123725,10 +134770,10 @@ realizes some 'host of immune response role' - glial cell line-derived neurotrophic factor - A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. + glial cell line-derived neurotrophic factor + A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. - glial cell line-derived neurotrophic factor + glial cell line-derived neurotrophic factor @@ -123737,10 +134782,10 @@ realizes some 'host of immune response role' - beta-globin - A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof. + beta-globin + A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof. - beta-globin + beta-globin @@ -123749,10 +134794,22 @@ realizes some 'host of immune response role' - haptoglobin - A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof. + haptoglobin + A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof. + + haptoglobin + + + + + + + + + leptin + A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof. - haptoglobin + leptin @@ -123761,10 +134818,10 @@ realizes some 'host of immune response role' - parathyroid hormone - A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof. + parathyroid hormone + A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof. - parathyroid hormone + parathyroid hormone @@ -123773,10 +134830,10 @@ realizes some 'host of immune response role' - ribonuclease T2 - A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. + ribonuclease T2 + A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. - ribonuclease T2 + ribonuclease T2 @@ -123785,10 +134842,10 @@ realizes some 'host of immune response role' - serotransferrin - A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof. + serotransferrin + A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof. - serotransferrin + serotransferrin @@ -123797,10 +134854,10 @@ realizes some 'host of immune response role' - transthyretin - A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof. + transthyretin + A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof. - transthyretin + transthyretin @@ -123821,12 +134878,12 @@ realizes some 'host of immune response role' - DNA ligase - A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. - Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule - ligase + DNA ligase + A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. + Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule + ligase - DNA ligase + DNA ligase @@ -123835,10 +134892,10 @@ realizes some 'host of immune response role' - T cell receptor co-receptor CD8 - A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. + T cell receptor co-receptor CD8 + A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. - T cell receptor co-receptor CD8 + T cell receptor co-receptor CD8 @@ -123847,10 +134904,10 @@ realizes some 'host of immune response role' - guanyl-specific ribonuclease T1 - A protein that is a translation product of the Aspergillus oryzae RIB40 rntA gene or a 1:1 ortholog thereof. + guanyl-specific ribonuclease T1 + A protein that is a translation product of the Aspergillus oryzae RIB40 rntA gene or a 1:1 ortholog thereof. - guanyl-specific ribonuclease T1 + guanyl-specific ribonuclease T1 @@ -123859,10 +134916,10 @@ realizes some 'host of immune response role' - nuclease S1 - A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof. + nuclease S1 + A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof. - nuclease S1 + nuclease S1 @@ -123871,10 +134928,10 @@ realizes some 'host of immune response role' - ribonuclease U2 - A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. + ribonuclease U2 + A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. - ribonuclease U2 + ribonuclease U2 @@ -123883,10 +134940,10 @@ realizes some 'host of immune response role' - ribonuclease V1 (cobra) - A protein with ribonuclease activity that is a constituent of cobra venom. + ribonuclease V1 (cobra) + A protein with ribonuclease activity that is a constituent of cobra venom. - ribonuclease V1 (cobra) + ribonuclease V1 (cobra) @@ -123895,10 +134952,10 @@ realizes some 'host of immune response role' - ribonuclease CL3 (chicken) - A protein with ribonuclease activity that is purified from chicken liver. + ribonuclease CL3 (chicken) + A protein with ribonuclease activity that is purified from chicken liver. - ribonuclease CL3 (chicken) + ribonuclease CL3 (chicken) @@ -123907,10 +134964,10 @@ realizes some 'host of immune response role' - cytosolic creatine kinase complex, MB-type - A cytosolic creatine kinase complex that is a heterodimer of a B-type subunit and an M-type subunit. + cytosolic creatine kinase complex, MB-type + A cytosolic creatine kinase complex that is a heterodimer of a B-type subunit and an M-type subunit. - cytosolic creatine kinase complex, MB-type + cytosolic creatine kinase complex, MB-type @@ -123919,10 +134976,10 @@ realizes some 'host of immune response role' - creatine kinase - A protein that contains a single ATP:guanido phosphotransferase N-terminal domain (Pfam:PF02807) followed by a single ATP:guanido phosphotransferase C-terminal catalytic domain (Pfam:PF00217). + creatine kinase + A protein that contains a single ATP:guanido phosphotransferase N-terminal domain (Pfam:PF02807) followed by a single ATP:guanido phosphotransferase C-terminal catalytic domain (Pfam:PF00217). - creatine kinase + creatine kinase @@ -123931,9 +134988,9 @@ realizes some 'host of immune response role' - protein-glutamine gamma-glutamyltransferase + protein-glutamine gamma-glutamyltransferase - protein-glutamine gamma-glutamyltransferase + protein-glutamine gamma-glutamyltransferase @@ -123942,10 +134999,10 @@ realizes some 'host of immune response role' - alanine aminotransferase - A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. + alanine aminotransferase + A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. - alanine aminotransferase + alanine aminotransferase @@ -123954,10 +135011,10 @@ realizes some 'host of immune response role' - lactate dehydrogenase complex - A protein-containing complex that is composed of four subunits of L-lactate dehydrogenase, cytoplasmic. + lactate dehydrogenase complex + A protein-containing complex that is composed of four subunits of L-lactate dehydrogenase, cytoplasmic. - lactate dehydrogenase complex + lactate dehydrogenase complex @@ -123966,10 +135023,10 @@ realizes some 'host of immune response role' - alkaline phosphatase (human) - A protein that is a translation product of any of the following alkaline phosphatase genes in human: ALPG (encoding the germinal form; GCAP), ALPP (encoding the placental form; PLAP), ALPI (encoding the intestinal form; IAP), and ALPL (encoding the tissue non-specific form; TNAP). + alkaline phosphatase (human) + A protein that is a translation product of any of the following alkaline phosphatase genes in human: ALPG (encoding the germinal form; GCAP), ALPP (encoding the placental form; PLAP), ALPI (encoding the intestinal form; IAP), and ALPL (encoding the tissue non-specific form; TNAP). - alkaline phosphatase (human) + alkaline phosphatase (human) @@ -123978,10 +135035,10 @@ realizes some 'host of immune response role' - aspartate aminotransferase (human) - A protein that is a translation product of any of the following genes in human: GOT1/GOT2. + aspartate aminotransferase (human) + A protein that is a translation product of any of the following genes in human: GOT1/GOT2. - aspartate aminotransferase (human) + aspartate aminotransferase (human) @@ -123990,10 +135047,10 @@ realizes some 'host of immune response role' - hemoglobin A1c - A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits. + hemoglobin A1c + A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits. - hemoglobin A1c + hemoglobin A1c @@ -124003,12 +135060,12 @@ realizes some 'host of immune response role' - A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. - Group: OBI - molecular tracer role - OBI developer call, 3-12-12 + A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. + Group: OBI + molecular tracer role + OBI developer call, 3-12-12 - obsolete molecular label role + obsolete molecular label role true @@ -124019,12 +135076,12 @@ realizes some 'host of immune response role' - A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay - Group: OBI - molecular tracer - OBI developer call, 3-12-12 + A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay + Group: OBI + molecular tracer + OBI developer call, 3-12-12 - obsolete molecular label + obsolete molecular label true @@ -124034,12 +135091,12 @@ realizes some 'host of immune response role' - region - A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. - primary structure of sequence macromolecule - sequence + region + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + primary structure of sequence macromolecule + sequence - region + region @@ -124048,11 +135105,11 @@ realizes some 'host of immune response role' - polypeptide - A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. - polypeptide sequence + polypeptide + A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. + polypeptide sequence - polypeptide + polypeptide @@ -124061,10 +135118,10 @@ realizes some 'host of immune response role' - supercontig - One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. + supercontig + One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. - supercontig + supercontig @@ -124073,10 +135130,10 @@ realizes some 'host of immune response role' - contig - A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + contig + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. - contig + contig @@ -124085,10 +135142,10 @@ realizes some 'host of immune response role' - miRNA - Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. + miRNA + Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. - miRNA + miRNA @@ -124097,10 +135154,10 @@ realizes some 'host of immune response role' - sequence_assembly - A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + sequence_assembly + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. - sequence_assembly + sequence_assembly @@ -124109,10 +135166,10 @@ realizes some 'host of immune response role' - circular - A quality of a nucleotide polymer that has no terminal nucleotide residues. + circular + A quality of a nucleotide polymer that has no terminal nucleotide residues. - circular + circular @@ -124121,10 +135178,10 @@ realizes some 'host of immune response role' - assembly - A region of the genome of known length that is composed by ordering and aligning two or more different regions. + assembly + A region of the genome of known length that is composed by ordering and aligning two or more different regions. - assembly + assembly @@ -124133,10 +135190,10 @@ realizes some 'host of immune response role' - experimental_feature - A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + experimental_feature + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. - experimental_feature + experimental_feature @@ -124145,10 +135202,10 @@ realizes some 'host of immune response role' - uterine cervix - Lower, narrow portion of the uterus where it joins with the top end of the vagina. + uterine cervix + Lower, narrow portion of the uterus where it joins with the top end of the vagina. - uterine cervix + uterine cervix @@ -124157,10 +135214,10 @@ realizes some 'host of immune response role' - pituitary gland - The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. + pituitary gland + The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. - pituitary gland + pituitary gland @@ -124169,10 +135226,10 @@ realizes some 'host of immune response role' - lymph node - Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. + lymph node + Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. - lymph node + lymph node @@ -124181,10 +135238,10 @@ realizes some 'host of immune response role' - urethra - the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening + urethra + the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening - urethra + urethra @@ -124193,10 +135250,10 @@ realizes some 'host of immune response role' - life cycle stage - A spatiotemporal region encompassing some part of the life cycle of an organism. + life cycle stage + A spatiotemporal region encompassing some part of the life cycle of an organism. - life cycle stage + life cycle stage @@ -124205,10 +135262,10 @@ realizes some 'host of immune response role' - mouth - The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + mouth + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - mouth + mouth @@ -124217,10 +135274,10 @@ realizes some 'host of immune response role' - amniotic fluid - Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. + amniotic fluid + Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. - amniotic fluid + amniotic fluid @@ -124229,10 +135286,10 @@ realizes some 'host of immune response role' - blood - A fluid that is composed of blood plasma and erythrocytes. + blood + A fluid that is composed of blood plasma and erythrocytes. - blood + blood @@ -124241,10 +135298,10 @@ realizes some 'host of immune response role' - breast - The upper ventral region of the torso of an organism. + breast + The upper ventral region of the torso of an organism. - breast + breast @@ -124253,10 +135310,10 @@ realizes some 'host of immune response role' - cervical mucus - A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. + cervical mucus + A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. - cervical mucus + cervical mucus @@ -124265,10 +135322,10 @@ realizes some 'host of immune response role' - throat - In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. + throat + In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. - throat + throat @@ -124277,10 +135334,10 @@ realizes some 'host of immune response role' - renal medulla - the inner portion of the kidney consisting of the renal pyramids + renal medulla + the inner portion of the kidney consisting of the renal pyramids - renal medulla + renal medulla @@ -124289,10 +135346,10 @@ realizes some 'host of immune response role' - organism substance - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. + organism substance + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance + organism substance @@ -124301,10 +135358,10 @@ realizes some 'host of immune response role' - material anatomical entity - Anatomical entity that has mass. + material anatomical entity + Anatomical entity that has mass. - material anatomical entity + material anatomical entity @@ -124313,10 +135370,10 @@ realizes some 'host of immune response role' - testis - A gonad of a male animal. A gonad produces and releases sperm. + testis + A gonad of a male animal. A gonad produces and releases sperm. - testis + testis @@ -124325,10 +135382,10 @@ realizes some 'host of immune response role' - anatomical cluster - Anatomical group that has its parts adjacent to one another. + anatomical cluster + Anatomical group that has its parts adjacent to one another. - anatomical cluster + anatomical cluster @@ -124337,10 +135394,10 @@ realizes some 'host of immune response role' - tissue - Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + tissue + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. - tissue + tissue @@ -124349,10 +135406,10 @@ realizes some 'host of immune response role' - multi-tissue structure - Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. + multi-tissue structure + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. - multi-tissue structure + multi-tissue structure @@ -124361,10 +135418,10 @@ realizes some 'host of immune response role' - epithelium - Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. + epithelium + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - epithelium + epithelium @@ -124373,10 +135430,10 @@ realizes some 'host of immune response role' - stomach - An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. + stomach + An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. - stomach + stomach @@ -124385,10 +135442,10 @@ realizes some 'host of immune response role' - aorta - The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation + aorta + The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation - aorta + aorta @@ -124397,10 +135454,10 @@ realizes some 'host of immune response role' - heart - A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. + heart + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. - heart + heart @@ -124409,10 +135466,10 @@ realizes some 'host of immune response role' - brain - The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. + brain + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. - brain + brain @@ -124421,10 +135478,10 @@ realizes some 'host of immune response role' - cerebral cortex - The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. + cerebral cortex + The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. - cerebral cortex + cerebral cortex @@ -124433,10 +135490,10 @@ realizes some 'host of immune response role' - eye - An organ that detects light. + eye + An organ that detects light. - eye + eye @@ -124445,10 +135502,10 @@ realizes some 'host of immune response role' - ovary - the gonad of a female organism which contains germ cells + ovary + the gonad of a female organism which contains germ cells - ovary + ovary @@ -124457,10 +135514,10 @@ realizes some 'host of immune response role' - uterus - the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth + uterus + the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth - uterus + uterus @@ -124469,10 +135526,10 @@ realizes some 'host of immune response role' - vagina - A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. + vagina + A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. - vagina + vagina @@ -124481,10 +135538,10 @@ realizes some 'host of immune response role' - respiratory system - Functional system which consists of structures involved in respiration. + respiratory system + Functional system which consists of structures involved in respiration. - respiratory system + respiratory system @@ -124493,10 +135550,10 @@ realizes some 'host of immune response role' - adipose tissue - Portion of connective tissue composed of adipocytes enmeshed in areolar tissue + adipose tissue + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue - adipose tissue + adipose tissue @@ -124505,10 +135562,10 @@ realizes some 'host of immune response role' - strand of hair - A filament, mostly protein, that grows from follicles found in the dermis[WP]. + strand of hair + A filament, mostly protein, that grows from follicles found in the dermis[WP]. - strand of hair + strand of hair @@ -124517,10 +135574,10 @@ realizes some 'host of immune response role' - rectum - the terminal portion of the intestinal tube, terminating with the anus + rectum + the terminal portion of the intestinal tube, terminating with the anus - rectum + rectum @@ -124529,10 +135586,10 @@ realizes some 'host of immune response role' - pleural fluid - Transudate contained in the pleural cavity. + pleural fluid + Transudate contained in the pleural cavity. - pleural fluid + pleural fluid @@ -124541,10 +135598,10 @@ realizes some 'host of immune response role' - urine - Excretion that is the output of a kidney + urine + Excretion that is the output of a kidney - urine + urine @@ -124553,10 +135610,10 @@ realizes some 'host of immune response role' - sweat - Secretion produced by a sweat gland. + sweat + Secretion produced by a sweat gland. - sweat + sweat @@ -124565,10 +135622,10 @@ realizes some 'host of immune response role' - synovial fluid - Joint fluid is a transudate of plasma that is actively secreted by synovial cells. + synovial fluid + Joint fluid is a transudate of plasma that is actively secreted by synovial cells. - synovial fluid + synovial fluid @@ -124577,10 +135634,10 @@ realizes some 'host of immune response role' - skeletal muscle tissue - Muscle tissue that consists primarily of skeletal muscle fibers. + skeletal muscle tissue + Muscle tissue that consists primarily of skeletal muscle fibers. - skeletal muscle tissue + skeletal muscle tissue @@ -124589,10 +135646,10 @@ realizes some 'host of immune response role' - colon - Last portion of the large intestine before it becomes the rectum. + colon + Last portion of the large intestine before it becomes the rectum. - colon + colon @@ -124601,10 +135658,10 @@ realizes some 'host of immune response role' - sigmoid colon - The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. + sigmoid colon + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. - sigmoid colon + sigmoid colon @@ -124613,10 +135670,10 @@ realizes some 'host of immune response role' - cortex of kidney - Outer cortical portion of the kidney, between the renal capsule and the renal medulla. + cortex of kidney + Outer cortical portion of the kidney, between the renal capsule and the renal medulla. - cortex of kidney + cortex of kidney @@ -124625,10 +135682,10 @@ realizes some 'host of immune response role' - urinary bladder - distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. + urinary bladder + distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. - urinary bladder + urinary bladder @@ -124637,10 +135694,10 @@ realizes some 'host of immune response role' - pancreas - An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. + pancreas + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. - pancreas + pancreas @@ -124649,10 +135706,10 @@ realizes some 'host of immune response role' - peritoneal fluid - Transudate contained in the peritoneal cavity. + peritoneal fluid + Transudate contained in the peritoneal cavity. - peritoneal fluid + peritoneal fluid @@ -124661,10 +135718,10 @@ realizes some 'host of immune response role' - tibial nerve - The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. + tibial nerve + The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. - tibial nerve + tibial nerve @@ -124673,10 +135730,10 @@ realizes some 'host of immune response role' - cerebrospinal fluid - A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + cerebrospinal fluid + A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. - cerebrospinal fluid + cerebrospinal fluid @@ -124685,10 +135742,10 @@ realizes some 'host of immune response role' - upper respiratory tract - The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. + upper respiratory tract + The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. - upper respiratory tract + upper respiratory tract @@ -124697,10 +135754,10 @@ realizes some 'host of immune response role' - lower respiratory tract - The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] + lower respiratory tract + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] - lower respiratory tract + lower respiratory tract @@ -124709,10 +135766,10 @@ realizes some 'host of immune response role' - cheek - A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. + cheek + A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. - cheek + cheek @@ -124721,10 +135778,10 @@ realizes some 'host of immune response role' - coronary artery - An artery that supplies the myocardium. + coronary artery + An artery that supplies the myocardium. - coronary artery + coronary artery @@ -124733,10 +135790,10 @@ realizes some 'host of immune response role' - vein - Any of the tubular branching vessels that carry blood from the capillaries toward the heart. + vein + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. - vein + vein @@ -124745,10 +135802,10 @@ realizes some 'host of immune response role' - tongue - A muscular organ in the floor of the mouth. + tongue + A muscular organ in the floor of the mouth. - tongue + tongue @@ -124757,10 +135814,10 @@ realizes some 'host of immune response role' - nasopharynx - the section of the pharynx that lies above the soft palate + nasopharynx + the section of the pharynx that lies above the soft palate - nasopharynx + nasopharynx @@ -124769,10 +135826,10 @@ realizes some 'host of immune response role' - oropharynx - the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis + oropharynx + the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis - oropharynx + oropharynx @@ -124781,10 +135838,10 @@ realizes some 'host of immune response role' - vitreous humor - A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina + vitreous humor + A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina - vitreous humor + vitreous humor @@ -124793,10 +135850,10 @@ realizes some 'host of immune response role' - nasal cavity mucosa - The mucous membrane that lines the nasal cavity[MP]. + nasal cavity mucosa + The mucous membrane that lines the nasal cavity[MP]. - nasal cavity mucosa + nasal cavity mucosa @@ -124805,10 +135862,10 @@ realizes some 'host of immune response role' - minor salivary gland - One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. + minor salivary gland + One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. - minor salivary gland + minor salivary gland @@ -124817,10 +135874,10 @@ realizes some 'host of immune response role' - saliva - A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + saliva + A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. - saliva + saliva @@ -124829,10 +135886,10 @@ realizes some 'host of immune response role' - caudate nucleus - Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. + caudate nucleus + Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. - caudate nucleus + caudate nucleus @@ -124841,10 +135898,10 @@ realizes some 'host of immune response role' - putamen - Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. + putamen + Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. - putamen + putamen @@ -124853,10 +135910,10 @@ realizes some 'host of immune response role' - milk - An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + milk + An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - milk + milk @@ -124865,10 +135922,10 @@ realizes some 'host of immune response role' - semen - Organism substance that is composed of sperm cells suspended in seminal fluid. + semen + Organism substance that is composed of sperm cells suspended in seminal fluid. - semen + semen @@ -124877,10 +135934,10 @@ realizes some 'host of immune response role' - bile - vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. + bile + vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. - bile + bile @@ -124889,10 +135946,10 @@ realizes some 'host of immune response role' - placenta - organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. + placenta + organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. - placenta + placenta @@ -124901,10 +135958,10 @@ realizes some 'host of immune response role' - feces - Portion of semisolid bodily waste discharged through the anus[MW,modified] + feces + Portion of semisolid bodily waste discharged through the anus[MW,modified] - feces + feces @@ -124913,10 +135970,10 @@ realizes some 'host of immune response role' - areola - Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. + areola + Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. - areola + areola @@ -124925,10 +135982,10 @@ realizes some 'host of immune response role' - cerebellum - Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. + cerebellum + Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. - cerebellum + cerebellum @@ -124937,10 +135994,10 @@ realizes some 'host of immune response role' - thyroid gland - A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. + thyroid gland + A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. - thyroid gland + thyroid gland @@ -124949,10 +136006,10 @@ realizes some 'host of immune response role' - lung - Respiration organ that develops as an outpocketing of the esophagus. + lung + Respiration organ that develops as an outpocketing of the esophagus. - lung + lung @@ -124961,10 +136018,10 @@ realizes some 'host of immune response role' - dermis - The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. + dermis + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. - dermis + dermis @@ -124973,10 +136030,10 @@ realizes some 'host of immune response role' - hypodermis - Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. + hypodermis + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. - hypodermis + hypodermis @@ -124985,10 +136042,10 @@ realizes some 'host of immune response role' - skin of body - The organ covering the body that consists of the dermis and epidermis. + skin of body + The organ covering the body that consists of the dermis and epidermis. - skin of body + skin of body @@ -124997,10 +136054,10 @@ realizes some 'host of immune response role' - spleen - the organ that functions to filter blood and to store red corpuscles and platelets + spleen + the organ that functions to filter blood and to store red corpuscles and platelets - spleen + spleen @@ -125009,10 +136066,10 @@ realizes some 'host of immune response role' - liver - An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. + liver + An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. - liver + liver @@ -125021,10 +136078,10 @@ realizes some 'host of immune response role' - ileum - the portion of the small intestine that extends from the jejunum to the colon + ileum + the portion of the small intestine that extends from the jejunum to the colon - ileum + ileum @@ -125033,10 +136090,10 @@ realizes some 'host of immune response role' - integument - The dermis, epidermis and hypodermis. + integument + The dermis, epidermis and hypodermis. - integument + integument @@ -125045,10 +136102,10 @@ realizes some 'host of immune response role' - peritoneum - A serous membrane that lines the peritoneal cavity[VHOG,modified]. + peritoneum + A serous membrane that lines the peritoneal cavity[VHOG,modified]. - peritoneum + peritoneum @@ -125057,10 +136114,10 @@ realizes some 'host of immune response role' - prostate gland - The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. + prostate gland + The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. - prostate gland + prostate gland @@ -125069,10 +136126,10 @@ realizes some 'host of immune response role' - adrenal gland - Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + adrenal gland + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - adrenal gland + adrenal gland @@ -125081,10 +136138,10 @@ realizes some 'host of immune response role' - bone marrow - the soft tissue that fills the cavities of bones + bone marrow + the soft tissue that fills the cavities of bones - bone marrow + bone marrow @@ -125093,10 +136150,10 @@ realizes some 'host of immune response role' - pericardial fluid - Transudate contained in the pericardial cavity.[FMA] + pericardial fluid + Transudate contained in the pericardial cavity.[FMA] - pericardial fluid + pericardial fluid @@ -125105,10 +136162,10 @@ realizes some 'host of immune response role' - tail - An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail + tail + An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail - tail + tail @@ -125117,10 +136174,10 @@ realizes some 'host of immune response role' - esophagus mucosa - A mucosa that is part of a esophagus [Automatically generated definition]. + esophagus mucosa + A mucosa that is part of a esophagus [Automatically generated definition]. - esophagus mucosa + esophagus mucosa @@ -125129,10 +136186,10 @@ realizes some 'host of immune response role' - left cerebral hemisphere - A cerebral hemisphere that is in the left side of a brain. + left cerebral hemisphere + A cerebral hemisphere that is in the left side of a brain. - left cerebral hemisphere + left cerebral hemisphere @@ -125141,10 +136198,10 @@ realizes some 'host of immune response role' - right cerebral hemisphere - A cerebral hemisphere that is in the right side of a brain. + right cerebral hemisphere + A cerebral hemisphere that is in the right side of a brain. - right cerebral hemisphere + right cerebral hemisphere @@ -125153,10 +136210,10 @@ realizes some 'host of immune response role' - trachea - The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. + trachea + The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. - trachea + trachea @@ -125165,10 +136222,10 @@ realizes some 'host of immune response role' - omentum - A fold of peritoneum originating at the stomach and supporting the viscera. + omentum + A fold of peritoneum originating at the stomach and supporting the viscera. - omentum + omentum @@ -125177,10 +136234,10 @@ realizes some 'host of immune response role' - esophagus muscularis mucosa - A muscularis mucosa that is part of a esophagus. + esophagus muscularis mucosa + A muscularis mucosa that is part of a esophagus. - esophagus muscularis mucosa + esophagus muscularis mucosa @@ -125189,10 +136246,10 @@ realizes some 'host of immune response role' - mucosa of nasopharynx - A mucosa that is part of a nasopharynx [Automatically generated definition]. + mucosa of nasopharynx + A mucosa that is part of a nasopharynx [Automatically generated definition]. - mucosa of nasopharynx + mucosa of nasopharynx @@ -125201,10 +136258,10 @@ realizes some 'host of immune response role' - mucosa of oropharynx - A mucosa that is part of a oropharynx [Automatically generated definition]. + mucosa of oropharynx + A mucosa that is part of a oropharynx [Automatically generated definition]. - mucosa of oropharynx + mucosa of oropharynx @@ -125213,10 +136270,10 @@ realizes some 'host of immune response role' - middle nasal concha - The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. + middle nasal concha + The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. - middle nasal concha + middle nasal concha @@ -125225,10 +136282,10 @@ realizes some 'host of immune response role' - bodily fluid - Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + bodily fluid + Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - bodily fluid + bodily fluid @@ -125237,10 +136294,10 @@ realizes some 'host of immune response role' - respiratory system fluid/secretion - A portion of organism substance that secreted_by a respiratory system. + respiratory system fluid/secretion + A portion of organism substance that secreted_by a respiratory system. - respiratory system fluid/secretion + respiratory system fluid/secretion @@ -125249,10 +136306,10 @@ realizes some 'host of immune response role' - atrium auricular region - A small conical pouch projections located on the upper anterior portion of each atrium of the heart. + atrium auricular region + A small conical pouch projections located on the upper anterior portion of each atrium of the heart. - atrium auricular region + atrium auricular region @@ -125261,9 +136318,9 @@ realizes some 'host of immune response role' - digestive system secreted substance + digestive system secreted substance - digestive system secreted substance + digestive system secreted substance @@ -125272,10 +136329,10 @@ realizes some 'host of immune response role' - chorionic villus - One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. + chorionic villus + One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. - chorionic villus + chorionic villus @@ -125284,10 +136341,10 @@ realizes some 'host of immune response role' - meconium - A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. + meconium + A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. - meconium + meconium @@ -125296,10 +136353,10 @@ realizes some 'host of immune response role' - sputum - Matter ejected from the lungs, bronchi, and trachea, through the mouth. + sputum + Matter ejected from the lungs, bronchi, and trachea, through the mouth. - sputum + sputum @@ -125308,10 +136365,10 @@ realizes some 'host of immune response role' - tibial artery - The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. + tibial artery + The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. - tibial artery + tibial artery @@ -125320,10 +136377,10 @@ realizes some 'host of immune response role' - esophagogastric junction - The junction between the esophagus and the stomach epithelium + esophagogastric junction + The junction between the esophagus and the stomach epithelium - esophagogastric junction + esophagogastric junction @@ -125332,10 +136389,10 @@ realizes some 'host of immune response role' - omental fat pad - encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon + omental fat pad + encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon - omental fat pad + omental fat pad @@ -125344,10 +136401,10 @@ realizes some 'host of immune response role' - umbilical cord blood - blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. + umbilical cord blood + blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. - umbilical cord blood + umbilical cord blood @@ -125356,10 +136413,10 @@ realizes some 'host of immune response role' - arterial blood - A blood that is part of a artery. + arterial blood + A blood that is part of a artery. - arterial blood + arterial blood @@ -125368,10 +136425,10 @@ realizes some 'host of immune response role' - venous blood - A blood that is part of a vein. + venous blood + A blood that is part of a vein. - venous blood + venous blood @@ -125380,10 +136437,10 @@ realizes some 'host of immune response role' - capillary blood - A blood that is part of a capillary. + capillary blood + A blood that is part of a capillary. - capillary blood + capillary blood @@ -125392,10 +136449,10 @@ realizes some 'host of immune response role' - suprapubic skin - Area of skin in the hypoastric region of the abdomen. + suprapubic skin + Area of skin in the hypoastric region of the abdomen. - suprapubic skin + suprapubic skin @@ -125404,10 +136461,10 @@ realizes some 'host of immune response role' - anterior nasal wall - Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. + anterior nasal wall + Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. - anterior nasal wall + anterior nasal wall @@ -125416,10 +136473,10 @@ realizes some 'host of immune response role' - length unit - A unit which is a standard measure of the distance between two points. + length unit + A unit which is a standard measure of the distance between two points. - length unit + length unit @@ -125428,10 +136485,10 @@ realizes some 'host of immune response role' - mass unit - A unit which is a standard measure of the amount of matter/energy of a physical object. + mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. - mass unit + mass unit @@ -125440,10 +136497,10 @@ realizes some 'host of immune response role' - time unit - A unit which is a standard measure of the dimension in which events occur in sequence. + time unit + A unit which is a standard measure of the dimension in which events occur in sequence. - time unit + time unit @@ -125452,9 +136509,9 @@ realizes some 'host of immune response role' - temperature unit + temperature unit - temperature unit + temperature unit @@ -125463,9 +136520,9 @@ realizes some 'host of immune response role' - substance unit + substance unit - substance unit + substance unit @@ -125474,9 +136531,9 @@ realizes some 'host of immune response role' - concentration unit + concentration unit - concentration unit + concentration unit @@ -125485,9 +136542,9 @@ realizes some 'host of immune response role' - volume unit + volume unit - volume unit + volume unit @@ -125496,9 +136553,9 @@ realizes some 'host of immune response role' - frequency unit + frequency unit - frequency unit + frequency unit @@ -125507,9 +136564,9 @@ realizes some 'host of immune response role' - pressure unit + pressure unit - pressure unit + pressure unit @@ -125518,9 +136575,9 @@ realizes some 'host of immune response role' - volumetric flow rate unit + volumetric flow rate unit - volumetric flow rate unit + volumetric flow rate unit @@ -125529,9 +136586,9 @@ realizes some 'host of immune response role' - rate unit + rate unit - rate unit + rate unit @@ -125564,7 +136621,7 @@ realizes some 'host of immune response role' - Obsolete Class + Obsolete Class @@ -125634,7 +136691,7 @@ realizes some 'host of immune response role' organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release - PERSON:Alan Ruttenberg + PERSON:Alan Ruttenberg organizational term @@ -125830,7 +136887,7 @@ realizes some 'host of immune response role' Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel - web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf + web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML @@ -125845,7 +136902,7 @@ realizes some 'host of immune response role' ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel - web-page:http://www.isac-net.org/content/view/607/150/ + web-page:http://www.isac-net.org/content/view/607/150/ ACS @@ -125860,7 +136917,7 @@ realizes some 'host of immune response role' XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel - web-page:http://www.w3.org/XML/ + web-page:http://www.w3.org/XML/ XML @@ -125875,7 +136932,7 @@ realizes some 'host of immune response role' RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel - web-page:http://www.w3.org/RDF/ + web-page:http://www.w3.org/RDF/ RDF @@ -125890,7 +136947,7 @@ realizes some 'host of immune response role' zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel - web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ + web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip @@ -125905,7 +136962,7 @@ realizes some 'host of immune response role' tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel - web-page:http://www.gnu.org/software/tar/manual/ + web-page:http://www.gnu.org/software/tar/manual/ tar @@ -125920,7 +136977,7 @@ realizes some 'host of immune response role' FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel - web-page:http://www.fcspress.com/ + web-page:http://www.fcspress.com/ FCS @@ -125935,7 +136992,7 @@ realizes some 'host of immune response role' Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel - web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf + web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML @@ -125950,7 +137007,7 @@ realizes some 'host of immune response role' Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel - web-page:http://www.flowcyt.org/gating/ + web-page:http://www.flowcyt.org/gating/ Gating-ML @@ -125965,7 +137022,7 @@ realizes some 'host of immune response role' OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel - web-page:http://www.w3.org/2004/OWL/ + web-page:http://www.w3.org/2004/OWL/ OWL @@ -125975,10 +137032,10 @@ realizes some 'host of immune response role' - obsolete_the supplier role of Affymetrix + obsolete_the supplier role of Affymetrix - obsolete_the supplier role of Affymetrix + obsolete_the supplier role of Affymetrix true @@ -125989,11 +137046,11 @@ realizes some 'host of immune response role' - Affymetrix - Affymetrix supplied microarray + Affymetrix + Affymetrix supplied microarray - An organization which supplies technology, tools and protocols for use in high throughput applications - Affymetrix + An organization which supplies technology, tools and protocols for use in high throughput applications + Affymetrix @@ -126002,10 +137059,10 @@ realizes some 'host of immune response role' - Thermo + Thermo - Philippe Rocca-Serra - Thermo + Philippe Rocca-Serra + Thermo @@ -126014,10 +137071,10 @@ realizes some 'host of immune response role' - Waters + Waters - Philippe Rocca-Serra - Waters + Philippe Rocca-Serra + Waters @@ -126026,10 +137083,10 @@ realizes some 'host of immune response role' - BIO-RAD + BIO-RAD - Philippe Rocca-Serra - BIO-RAD + Philippe Rocca-Serra + BIO-RAD @@ -126038,10 +137095,10 @@ realizes some 'host of immune response role' - GenePattern hierarchical clustering + GenePattern hierarchical clustering - James Malone - GenePattern hierarchical clustering + James Malone + GenePattern hierarchical clustering @@ -126050,10 +137107,10 @@ realizes some 'host of immune response role' - Ambion + Ambion - Philippe Rocca-Serra - Ambion + Philippe Rocca-Serra + Ambion @@ -126062,10 +137119,10 @@ realizes some 'host of immune response role' - Helicos + Helicos - Philippe Rocca-Serra - Helicos + Philippe Rocca-Serra + Helicos @@ -126074,10 +137131,10 @@ realizes some 'host of immune response role' - Roche + Roche - Philippe Rocca-Serra - Roche + Philippe Rocca-Serra + Roche @@ -126086,10 +137143,10 @@ realizes some 'host of immune response role' - Illumina + Illumina - Philippe Rocca-Serra - Illumina + Philippe Rocca-Serra + Illumina @@ -126098,9 +137155,9 @@ realizes some 'host of immune response role' - GenePattern PCA + GenePattern PCA - GenePattern PCA + GenePattern PCA @@ -126110,12 +137167,12 @@ realizes some 'host of immune response role' - GenePattern module SVM + GenePattern module SVM - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. - James Malone - Ryan Brinkman - GenePattern module SVM + GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + James Malone + Ryan Brinkman + GenePattern module SVM @@ -126124,10 +137181,10 @@ realizes some 'host of immune response role' - GenePattern k-nearest neighbors + GenePattern k-nearest neighbors - James Malone - GenePattern k-nearest neighbors + James Malone + GenePattern k-nearest neighbors @@ -126136,9 +137193,9 @@ realizes some 'host of immune response role' - GenePattern LOOCV + GenePattern LOOCV - GenePattern LOOCV + GenePattern LOOCV @@ -126147,10 +137204,10 @@ realizes some 'host of immune response role' - GenePattern k-means clustering + GenePattern k-means clustering - James Malone - GenePattern k-means clustering + James Malone + GenePattern k-means clustering @@ -126159,10 +137216,10 @@ realizes some 'host of immune response role' - Agilent + Agilent - Philippe Rocca-Serra - Agilent + Philippe Rocca-Serra + Agilent @@ -126172,12 +137229,12 @@ realizes some 'host of immune response role' - GenePattern module KMeansClustering + GenePattern module KMeansClustering - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. - James Malone - PERSON: James Malone - GenePattern module KMeansClustering + GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module KMeansClustering @@ -126186,10 +137243,10 @@ realizes some 'host of immune response role' - GenePattern CART + GenePattern CART - James Malone - GenePattern CART + James Malone + GenePattern CART @@ -126200,10 +137257,10 @@ realizes some 'host of immune response role' - GenePattern module CARTXValidation + GenePattern module CARTXValidation - GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. - GenePattern module CARTXValidation + GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. + GenePattern module CARTXValidation @@ -126212,10 +137269,10 @@ realizes some 'host of immune response role' - Li-Cor + Li-Cor - Philippe Rocca-Serra - Li-Cor + Philippe Rocca-Serra + Li-Cor @@ -126224,10 +137281,10 @@ realizes some 'host of immune response role' - Bruker Corporation + Bruker Corporation - Philippe Rocca-Serra - Bruker Corporation + Philippe Rocca-Serra + Bruker Corporation @@ -126236,12 +137293,12 @@ realizes some 'host of immune response role' - GenePattern module KNNXValidation + GenePattern module KNNXValidation - GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. - James Malone - PERSON: James Malone - GenePattern module KNNXValidation + GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. + James Malone + PERSON: James Malone + GenePattern module KNNXValidation @@ -126251,9 +137308,9 @@ realizes some 'host of immune response role' - GenePattern module PeakMatch + GenePattern module PeakMatch - GenePattern module PeakMatch + GenePattern module PeakMatch @@ -126263,11 +137320,11 @@ realizes some 'host of immune response role' - GenePattern module KNN + GenePattern module KNN - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. - James Malone - GenePattern module KNN + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + James Malone + GenePattern module KNN @@ -126277,12 +137334,12 @@ realizes some 'host of immune response role' - GenePattern module HierarchicalClustering + GenePattern module HierarchicalClustering - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. - James Malone - PERSON: James Malone - GenePattern module HierarchicalClustering + GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module HierarchicalClustering @@ -126291,10 +137348,10 @@ realizes some 'host of immune response role' - GenePattern SVM + GenePattern SVM - James Malone - GenePattern SVM + James Malone + GenePattern SVM @@ -126303,10 +137360,10 @@ realizes some 'host of immune response role' - Applied Biosystems + Applied Biosystems - Philippe Rocca-Serra - Applied Biosystems + Philippe Rocca-Serra + Applied Biosystems @@ -126316,12 +137373,12 @@ realizes some 'host of immune response role' - GenePattern module PCA + GenePattern module PCA - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. - James Malone - PERSON: James Malone - GenePattern module PCA + GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + James Malone + PERSON: James Malone + GenePattern module PCA @@ -126330,11 +137387,11 @@ realizes some 'host of immune response role' - GenePattern peak matching + GenePattern peak matching - James Malone - Ryan Brinkman - GenePattern peak matching + James Malone + Ryan Brinkman + GenePattern peak matching @@ -126343,10 +137400,10 @@ realizes some 'host of immune response role' - Bruker Daltonics + Bruker Daltonics - Philippe Rocca-Serra - Bruker Daltonics + Philippe Rocca-Serra + Bruker Daltonics @@ -126355,11 +137412,11 @@ realizes some 'host of immune response role' - GenePattern HeatMapViewer data visualization + GenePattern HeatMapViewer data visualization - The GenePattern process of generating Heat Maps from clustered data. - James Malone - GenePattern HeatMapViewer data visualization + The GenePattern process of generating Heat Maps from clustered data. + James Malone + GenePattern HeatMapViewer data visualization @@ -126368,11 +137425,11 @@ realizes some 'host of immune response role' - GenePattern HierarchicalClusteringViewer data visualization + GenePattern HierarchicalClusteringViewer data visualization - The GenePattern process of generating hierarchical clustering visualization from clustered data. - James Malone - GenePattern HierarchicalClusteringViewer data visualization + The GenePattern process of generating hierarchical clustering visualization from clustered data. + James Malone + GenePattern HierarchicalClusteringViewer data visualization @@ -126382,11 +137439,11 @@ realizes some 'host of immune response role' - GenePattern module HeatMapViewer + GenePattern module HeatMapViewer - A GenePattern software module which is used to generate a heatmap view of data. - James Malone - GenePattern module HeatMapViewer + A GenePattern software module which is used to generate a heatmap view of data. + James Malone + GenePattern module HeatMapViewer @@ -126396,11 +137453,11 @@ realizes some 'host of immune response role' - GenePattern module HierarchicalClusteringViewer + GenePattern module HierarchicalClusteringViewer - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. - James Malone - GenePattern module HierarchicalClusteringViewer + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + James Malone + GenePattern module HierarchicalClusteringViewer @@ -126409,10 +137466,10 @@ realizes some 'host of immune response role' - Sysmex Corporation, Kobe, Japan + Sysmex Corporation, Kobe, Japan - WEB:http://www.sysmex.com/@2009/08/06 - Sysmex Corporation, Kobe, Japan + WEB:http://www.sysmex.com/@2009/08/06 + Sysmex Corporation, Kobe, Japan @@ -126421,10 +137478,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Agilent + obsolete_the manufacturer role of Agilent - obsolete_the manufacturer role of Agilent + obsolete_the manufacturer role of Agilent true @@ -126434,10 +137491,10 @@ realizes some 'host of immune response role' - obsolete_manufacturer role of Bruker Daltonics + obsolete_manufacturer role of Bruker Daltonics - obsolete_manufacturer role of Bruker Daltonics + obsolete_manufacturer role of Bruker Daltonics true @@ -126447,10 +137504,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Thermo + obsolete_the manufacturer role of Thermo - obsolete_the manufacturer role of Thermo + obsolete_the manufacturer role of Thermo true @@ -126460,10 +137517,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Li-Cor + obsolete_the manufacturer role of Li-Cor - obsolete_the manufacturer role of Li-Cor + obsolete_the manufacturer role of Li-Cor true @@ -126473,10 +137530,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Roche + obsolete_the manufacturer role of Roche - obsolete_the manufacturer role of Roche + obsolete_the manufacturer role of Roche true @@ -126486,10 +137543,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Ambion + obsolete_the manufacturer role of Ambion - obsolete_the manufacturer role of Ambion + obsolete_the manufacturer role of Ambion true @@ -126499,10 +137556,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of BIO-RAD + obsolete_the manufacturer role of BIO-RAD - obsolete_the manufacturer role of BIO-RAD + obsolete_the manufacturer role of BIO-RAD true @@ -126512,10 +137569,10 @@ realizes some 'host of immune response role' - obsolete_the regulator role of the FDA + obsolete_the regulator role of the FDA - obsolete_the regulator role of the FDA + obsolete_the regulator role of the FDA true @@ -126525,10 +137582,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Illumina + obsolete_the manufacturer role of Illumina - obsolete_the manufacturer role of Illumina + obsolete_the manufacturer role of Illumina true @@ -126538,10 +137595,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Helicos + obsolete_the manufacturer role of Helicos - obsolete_the manufacturer role of Helicos + obsolete_the manufacturer role of Helicos true @@ -126551,10 +137608,10 @@ realizes some 'host of immune response role' - obsolete_manufacturer role of Bruker Corporation + obsolete_manufacturer role of Bruker Corporation - obsolete_manufacturer role of Bruker Corporation + obsolete_manufacturer role of Bruker Corporation true @@ -126564,10 +137621,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Waters + obsolete_the manufacturer role of Waters - obsolete_the manufacturer role of Waters + obsolete_the manufacturer role of Waters true @@ -126577,10 +137634,10 @@ realizes some 'host of immune response role' - obsolete_manufacturer role of applied biosystems + obsolete_manufacturer role of applied biosystems - obsolete_manufacturer role of applied biosystems + obsolete_manufacturer role of applied biosystems true @@ -126590,10 +137647,10 @@ realizes some 'host of immune response role' - U.S. Food and Drug Administration + U.S. Food and Drug Administration - FDA - U.S. Food and Drug Administration + FDA + U.S. Food and Drug Administration @@ -126602,9 +137659,9 @@ realizes some 'host of immune response role' - right handed + right handed - right handed + right handed @@ -126613,9 +137670,9 @@ realizes some 'host of immune response role' - ambidexterous + ambidexterous - ambidexterous + ambidexterous @@ -126624,9 +137681,9 @@ realizes some 'host of immune response role' - left handed + left handed - left handed + left handed @@ -126635,14 +137692,14 @@ realizes some 'host of immune response role' - Edingburgh handedness inventory + Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. - PERSON:Alan Ruttenberg - PERSON:Jessica Turner - PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 - WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html - Edingburgh handedness inventory + PERSON:Alan Ruttenberg + PERSON:Jessica Turner + PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 + WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html + Edingburgh handedness inventory @@ -126651,12 +137708,12 @@ realizes some 'host of immune response role' - eBioscience + eBioscience - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.ebioscience.com/@2011/04/11 - eBioscience + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.ebioscience.com/@2011/04/11 + eBioscience @@ -126665,12 +137722,12 @@ realizes some 'host of immune response role' - Cytopeia + Cytopeia - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.cytopeia.com/@2011/04/11 - Cytopeia + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.cytopeia.com/@2011/04/11 + Cytopeia @@ -126679,12 +137736,12 @@ realizes some 'host of immune response role' - Exalpha Biological + Exalpha Biological - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.exalpha.com/@2011/04/11 - Exalpha Biological + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.exalpha.com/@2011/04/11 + Exalpha Biological @@ -126693,12 +137750,12 @@ realizes some 'host of immune response role' - Apogee Flow Systems + Apogee Flow Systems - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.apogeeflow.com/@2011/04/11 - Apogee Flow Systems + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.apogeeflow.com/@2011/04/11 + Apogee Flow Systems @@ -126707,12 +137764,12 @@ realizes some 'host of immune response role' - Exbio Antibodies + Exbio Antibodies - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.exbio.cz/@2011/04/11 - Exbio Antibodies + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.exbio.cz/@2011/04/11 + Exbio Antibodies @@ -126721,12 +137778,12 @@ realizes some 'host of immune response role' - Becton Dickinson (BD Biosciences) + Becton Dickinson (BD Biosciences) - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.bdbiosciences.com/@2011/04/11 - Becton Dickinson (BD Biosciences) + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.bdbiosciences.com/@2011/04/11 + Becton Dickinson (BD Biosciences) @@ -126735,12 +137792,12 @@ realizes some 'host of immune response role' - Dako Cytomation + Dako Cytomation - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.dakousa.com/@2011/04/11 - Dako Cytomation + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.dakousa.com/@2011/04/11 + Dako Cytomation @@ -126749,12 +137806,12 @@ realizes some 'host of immune response role' - Millipore + Millipore - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.guavatechnologies.com/@2011/04/11 - Millipore + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.guavatechnologies.com/@2011/04/11 + Millipore @@ -126763,12 +137820,12 @@ realizes some 'host of immune response role' - Antigenix + Antigenix - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.antigenix.com/@2011/04/11 - Antigenix + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.antigenix.com/@2011/04/11 + Antigenix @@ -126777,12 +137834,12 @@ realizes some 'host of immune response role' - Partec + Partec - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.partec.de/@2011/04/11 - Partec + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.partec.de/@2011/04/11 + Partec @@ -126791,12 +137848,12 @@ realizes some 'host of immune response role' - Beckman Coulter + Beckman Coulter - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.beckmancoulter.com/@2011/04/11 - Beckman Coulter + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.beckmancoulter.com/@2011/04/11 + Beckman Coulter @@ -126805,12 +137862,12 @@ realizes some 'host of immune response role' - Advanced Instruments Inc. (AI Companies) + Advanced Instruments Inc. (AI Companies) - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.aicompanies.com/@2011/04/11 - Advanced Instruments Inc. (AI Companies) + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.aicompanies.com/@2011/04/11 + Advanced Instruments Inc. (AI Companies) @@ -126819,12 +137876,12 @@ realizes some 'host of immune response role' - Miltenyi Biotec + Miltenyi Biotec - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.miltenyibiotec.com/@2011/04/11 - Miltenyi Biotec + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.miltenyibiotec.com/@2011/04/11 + Miltenyi Biotec @@ -126833,12 +137890,12 @@ realizes some 'host of immune response role' - AES Chemunex + AES Chemunex - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.aeschemunex.com/@2011/04/11 - AES Chemunex + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.aeschemunex.com/@2011/04/11 + AES Chemunex @@ -126847,12 +137904,12 @@ realizes some 'host of immune response role' - Bentley Instruments + Bentley Instruments - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://bentleyinstruments.com/@2011/04/11 - Bentley Instruments + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://bentleyinstruments.com/@2011/04/11 + Bentley Instruments @@ -126861,12 +137918,12 @@ realizes some 'host of immune response role' - Invitrogen + Invitrogen - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.invitrogen.com/@2011/04/11 - Invitrogen + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.invitrogen.com/@2011/04/11 + Invitrogen @@ -126875,12 +137932,12 @@ realizes some 'host of immune response role' - Luminex + Luminex - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.luminexcorp.com/@2011/04/11 - Luminex + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.luminexcorp.com/@2011/04/11 + Luminex @@ -126889,12 +137946,12 @@ realizes some 'host of immune response role' - CytoBuoy + CytoBuoy - A supplier of flow cytometry analyzers - Karin Breuer - WEB:http://www.cytobuoy.com/@2011/04/11 - CytoBuoy + A supplier of flow cytometry analyzers + Karin Breuer + WEB:http://www.cytobuoy.com/@2011/04/11 + CytoBuoy @@ -126903,11 +137960,11 @@ realizes some 'host of immune response role' - Nimblegen + Nimblegen - An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. - Person: Jie Zheng - Nimblegen + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + Person: Jie Zheng + Nimblegen @@ -126916,11 +137973,11 @@ realizes some 'host of immune response role' - Pacific Biosciences + Pacific Biosciences - An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. - Person: Jie Zheng - Pacific Biosciences + An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. + Person: Jie Zheng + Pacific Biosciences @@ -126929,10 +137986,10 @@ realizes some 'host of immune response role' - NanoString Technologies + NanoString Technologies - An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. - NanoString Technologies + An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. + NanoString Technologies @@ -126941,12 +137998,12 @@ realizes some 'host of immune response role' - Thermo Fisher Scientific + Thermo Fisher Scientific - An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific - Thermo Fisher Scientific + An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific + Thermo Fisher Scientific @@ -126957,11 +138014,11 @@ realizes some 'host of immune response role' G1: Well differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. - Chris Stoeckert, Helena Ellis - G1 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB + A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + Chris Stoeckert, Helena Ellis + G1 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB G1: Well differentiated @@ -126973,11 +138030,11 @@ realizes some 'host of immune response role' G2: Moderately differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. - Chris Stoeckert, Helena Ellis - G2 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB + A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + Chris Stoeckert, Helena Ellis + G2 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB G2: Moderately differentiated @@ -126989,11 +138046,11 @@ realizes some 'host of immune response role' G3: Poorly differentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. - Chris Stoeckert, Helena Ellis - G3 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB + A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G3 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB G3: Poorly differentiated @@ -127005,11 +138062,11 @@ realizes some 'host of immune response role' G4: Undifferentiated - A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. - Chris Stoeckert, Helena Ellis - G4 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB + A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G4 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB G4: Undifferentiated @@ -127021,11 +138078,11 @@ realizes some 'host of immune response role' G1 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. - Chris Stoeckert, Helena Ellis - Grade 1 - NCI BBRB, OBI - NCI BBRB + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. + Chris Stoeckert, Helena Ellis + Grade 1 + NCI BBRB, OBI + NCI BBRB G1 (Fuhrman) @@ -127037,11 +138094,11 @@ realizes some 'host of immune response role' G2 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. - Chris Stoeckert, Helena Ellis - Grade 2 - NCI BBRB, OBI - NCI BBRB + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + Chris Stoeckert, Helena Ellis + Grade 2 + NCI BBRB, OBI + NCI BBRB G2 (Fuhrman) @@ -127053,11 +138110,11 @@ realizes some 'host of immune response role' G3 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. - Chris Stoeckert, Helena Ellis - Grade 3 - NCI BBRB, OBI - NCI BBRB + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + Chris Stoeckert, Helena Ellis + Grade 3 + NCI BBRB, OBI + NCI BBRB G3 (Fuhrman) @@ -127069,11 +138126,11 @@ realizes some 'host of immune response role' G4 (Fuhrman) - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. - Chris Stoeckert, Helena Ellis - Grade 4 - NCI BBRB, OBI - NCI BBRB + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. + Chris Stoeckert, Helena Ellis + Grade 4 + NCI BBRB, OBI + NCI BBRB G4 (Fuhrman) @@ -127085,11 +138142,11 @@ realizes some 'host of immune response role' Low grade ovarian tumor - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. - Chris Stoeckert, Helena Ellis - Low grade - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + Chris Stoeckert, Helena Ellis + Low grade + NCI BBRB, OBI + NCI BBRB Low grade ovarian tumor @@ -127101,11 +138158,11 @@ realizes some 'host of immune response role' High grade ovarian tumor - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. - Chris Stoeckert, Helena Ellis - High grade - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + Chris Stoeckert, Helena Ellis + High grade + NCI BBRB, OBI + NCI BBRB High grade ovarian tumor @@ -127117,11 +138174,11 @@ realizes some 'host of immune response role' G1 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. - Chris Stoeckert, Helena Ellis - G1 - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + Chris Stoeckert, Helena Ellis + G1 + NCI BBRB, OBI + NCI BBRB G1 (WHO) @@ -127133,11 +138190,11 @@ realizes some 'host of immune response role' G2 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. - Chris Stoeckert, Helena Ellis - G2 - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + Chris Stoeckert, Helena Ellis + G2 + NCI BBRB, OBI + NCI BBRB G2 (WHO) @@ -127149,11 +138206,11 @@ realizes some 'host of immune response role' G3 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. - Chris Stoeckert, Helena Ellis - G3 - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + Chris Stoeckert, Helena Ellis + G3 + NCI BBRB, OBI + NCI BBRB G3 (WHO) @@ -127165,11 +138222,11 @@ realizes some 'host of immune response role' G4 (WHO) - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. - Chris Stoeckert, Helena Ellis - G4 - NCI BBRB, OBI - NCI BBRB + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + Chris Stoeckert, Helena Ellis + G4 + NCI BBRB, OBI + NCI BBRB G4 (WHO) @@ -127181,10 +138238,10 @@ realizes some 'host of immune response role' pT0 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pT0 (colon) @@ -127196,10 +138253,10 @@ realizes some 'host of immune response role' pTis (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pTis (colon) @@ -127211,10 +138268,10 @@ realizes some 'host of immune response role' pT1 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pT1 (colon) @@ -127226,10 +138283,10 @@ realizes some 'host of immune response role' pT2 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pT2 (colon) @@ -127241,10 +138298,10 @@ realizes some 'host of immune response role' pT3 (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pT3 (colon) @@ -127256,10 +138313,10 @@ realizes some 'host of immune response role' pT4a (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pT4a (colon) @@ -127271,10 +138328,10 @@ realizes some 'host of immune response role' pT4b (colon) - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB pT4b (colon) @@ -127286,10 +138343,10 @@ realizes some 'host of immune response role' pT0 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT0 (lung) @@ -127301,10 +138358,10 @@ realizes some 'host of immune response role' pTis (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pTis (lung) @@ -127316,10 +138373,10 @@ realizes some 'host of immune response role' pT1 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT1 (lung) @@ -127331,10 +138388,10 @@ realizes some 'host of immune response role' pT1a (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT1a (lung) @@ -127346,10 +138403,10 @@ realizes some 'host of immune response role' pT1b (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT1b (lung) @@ -127361,10 +138418,10 @@ realizes some 'host of immune response role' pT2 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT2 (lung) @@ -127376,10 +138433,10 @@ realizes some 'host of immune response role' pT2a (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT2a (lung) @@ -127391,10 +138448,10 @@ realizes some 'host of immune response role' pT2b (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT2b (lung) @@ -127406,10 +138463,10 @@ realizes some 'host of immune response role' pT3 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT3 (lung) @@ -127421,10 +138478,10 @@ realizes some 'host of immune response role' pT4 (lung) - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB pT4 (lung) @@ -127436,10 +138493,10 @@ realizes some 'host of immune response role' pT0 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT0 (kidney) @@ -127451,10 +138508,10 @@ realizes some 'host of immune response role' pT1 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT1 (kidney) @@ -127466,10 +138523,10 @@ realizes some 'host of immune response role' pT1a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT1a (kidney) @@ -127481,10 +138538,10 @@ realizes some 'host of immune response role' pT1b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT1b (kidney) @@ -127496,10 +138553,10 @@ realizes some 'host of immune response role' pT2 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT2 (kidney) @@ -127511,10 +138568,10 @@ realizes some 'host of immune response role' pT2a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT2a (kidney) @@ -127526,10 +138583,10 @@ realizes some 'host of immune response role' pT2b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT2b (kidney) @@ -127541,10 +138598,10 @@ realizes some 'host of immune response role' pT3 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT3 (kidney) @@ -127556,10 +138613,10 @@ realizes some 'host of immune response role' pT3a (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT3a (kidney) @@ -127571,10 +138628,10 @@ realizes some 'host of immune response role' pT3b (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT3b (kidney) @@ -127586,10 +138643,10 @@ realizes some 'host of immune response role' pT3c (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT3c (kidney) @@ -127601,10 +138658,10 @@ realizes some 'host of immune response role' pT4 (kidney) - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB pT4 (kidney) @@ -127616,10 +138673,10 @@ realizes some 'host of immune response role' pT0 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT0 (ovary) @@ -127631,10 +138688,10 @@ realizes some 'host of immune response role' pT1 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT1 (ovary) @@ -127646,10 +138703,10 @@ realizes some 'host of immune response role' pT1a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT1a (ovary) @@ -127661,10 +138718,10 @@ realizes some 'host of immune response role' pT1b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT1b (ovary) @@ -127676,10 +138733,10 @@ realizes some 'host of immune response role' pT1c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT1c (ovary) @@ -127691,10 +138748,10 @@ realizes some 'host of immune response role' pT2 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT2 (ovary) @@ -127706,10 +138763,10 @@ realizes some 'host of immune response role' pT2a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT2a (ovary) @@ -127721,10 +138778,10 @@ realizes some 'host of immune response role' pT2b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT2b (ovary) @@ -127736,10 +138793,10 @@ realizes some 'host of immune response role' pT2c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT2c (ovary) @@ -127751,10 +138808,10 @@ realizes some 'host of immune response role' pT3 (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT3 (ovary) @@ -127766,10 +138823,10 @@ realizes some 'host of immune response role' pT3a (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT3a (ovary) @@ -127781,10 +138838,10 @@ realizes some 'host of immune response role' pT3b (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT3b (ovary) @@ -127796,10 +138853,10 @@ realizes some 'host of immune response role' pT3c (ovary) - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB pT3c (ovary) @@ -127811,10 +138868,10 @@ realizes some 'host of immune response role' pN0 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN0 (colon) @@ -127826,10 +138883,10 @@ realizes some 'host of immune response role' pN1 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN1 (colon) @@ -127841,10 +138898,10 @@ realizes some 'host of immune response role' pN1a (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN1a (colon) @@ -127856,10 +138913,10 @@ realizes some 'host of immune response role' pN1b (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN1b (colon) @@ -127871,10 +138928,10 @@ realizes some 'host of immune response role' pN1c (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN1c (colon) @@ -127886,10 +138943,10 @@ realizes some 'host of immune response role' pN2 (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN2 (colon) @@ -127901,10 +138958,10 @@ realizes some 'host of immune response role' pN2a (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN2a (colon) @@ -127916,10 +138973,10 @@ realizes some 'host of immune response role' pN2b (colon) - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB pN2b (colon) @@ -127931,10 +138988,10 @@ realizes some 'host of immune response role' pN0 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB + A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB pN0 (lung) @@ -127946,10 +139003,10 @@ realizes some 'host of immune response role' pN1 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB pN1 (lung) @@ -127961,10 +139018,10 @@ realizes some 'host of immune response role' pN2 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB pN2 (lung) @@ -127976,10 +139033,10 @@ realizes some 'host of immune response role' pN3 (lung) - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB pN3 (lung) @@ -127991,10 +139048,10 @@ realizes some 'host of immune response role' pN0 (kidney) - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ - NCI BBRB + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB pN0 (kidney) @@ -128006,10 +139063,10 @@ realizes some 'host of immune response role' pN1 (kidney) - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ - NCI BBRB + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB pN1 (kidney) @@ -128021,10 +139078,10 @@ realizes some 'host of immune response role' pN0 (ovary) - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ - NCI BBRB + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB pN0 (ovary) @@ -128036,10 +139093,10 @@ realizes some 'host of immune response role' pN1 (ovary) - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ - NCI BBRB + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB pN1 (ovary) @@ -128051,10 +139108,10 @@ realizes some 'host of immune response role' cM0 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB cM0 (colon) @@ -128066,10 +139123,10 @@ realizes some 'host of immune response role' cM1 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB cM1 (colon) @@ -128081,10 +139138,10 @@ realizes some 'host of immune response role' cM1a (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB cM1a (colon) @@ -128096,10 +139153,10 @@ realizes some 'host of immune response role' cM1b (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB cM1b (colon) @@ -128111,10 +139168,10 @@ realizes some 'host of immune response role' pM1 (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB pM1 (colon) @@ -128126,10 +139183,10 @@ realizes some 'host of immune response role' pM1a (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB pM1a (colon) @@ -128141,10 +139198,10 @@ realizes some 'host of immune response role' pM1b (colon) - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB pM1b (colon) @@ -128156,10 +139213,10 @@ realizes some 'host of immune response role' cM0 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB cM0 (lung) @@ -128171,10 +139228,10 @@ realizes some 'host of immune response role' cM1 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB cM1 (lung) @@ -128186,10 +139243,10 @@ realizes some 'host of immune response role' cM1a (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB cM1a (lung) @@ -128201,10 +139258,10 @@ realizes some 'host of immune response role' cM1b (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB cM1b (lung) @@ -128216,10 +139273,10 @@ realizes some 'host of immune response role' pM1 (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB pM1 (lung) @@ -128231,10 +139288,10 @@ realizes some 'host of immune response role' pM1a (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB pM1a (lung) @@ -128246,10 +139303,10 @@ realizes some 'host of immune response role' pM1b (lung) - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB pM1b (lung) @@ -128261,10 +139318,10 @@ realizes some 'host of immune response role' cM0 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB cM0 (kidney) @@ -128276,10 +139333,10 @@ realizes some 'host of immune response role' cM1 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB cM1 (kidney) @@ -128291,10 +139348,10 @@ realizes some 'host of immune response role' pM1 (kidney) - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB pM1 (kidney) @@ -128306,10 +139363,10 @@ realizes some 'host of immune response role' cM0 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB cM0 (ovary) @@ -128321,10 +139378,10 @@ realizes some 'host of immune response role' cM1 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB cM1 (ovary) @@ -128336,10 +139393,10 @@ realizes some 'host of immune response role' pM1 (ovary) - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB pM1 (ovary) @@ -128351,11 +139408,11 @@ realizes some 'host of immune response role' Occult Carcinoma (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. - Chris Stoeckert, Helena Ellis - Occult Carcinoma - http://www.medilexicon.com/dictionary/14371 - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. + Chris Stoeckert, Helena Ellis + Occult Carcinoma + http://www.medilexicon.com/dictionary/14371 + NCI BBRB Occult Carcinoma (AJCC 7th) @@ -128367,11 +139424,11 @@ realizes some 'host of immune response role' Stage 0 (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. - Chris Stoeckert, Helena Ellis - Stage 0 - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. + Chris Stoeckert, Helena Ellis + Stage 0 + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage 0 (AJCC 7th) @@ -128383,11 +139440,11 @@ realizes some 'host of immune response role' Stage I (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. - Chris Stoeckert, Helena Ellis - Stage I - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + Chris Stoeckert, Helena Ellis + Stage I + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage I (AJCC 7th) @@ -128399,11 +139456,11 @@ realizes some 'host of immune response role' Stage IIA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. - Chris Stoeckert, Helena Ellis - Stage IIA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IIA (AJCC 7th) @@ -128415,11 +139472,11 @@ realizes some 'host of immune response role' Stage IIB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. - Chris Stoeckert, Helena Ellis - Stage IIB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IIB (AJCC 7th) @@ -128431,11 +139488,11 @@ realizes some 'host of immune response role' Stage IIC (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. - Chris Stoeckert, Helena Ellis - Stage IIC - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. + Chris Stoeckert, Helena Ellis + Stage IIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IIC (AJCC 7th) @@ -128447,11 +139504,11 @@ realizes some 'host of immune response role' Stage IIIA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. - Chris Stoeckert, Helena Ellis - Stage IIIA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IIIA (AJCC 7th) @@ -128463,11 +139520,11 @@ realizes some 'host of immune response role' Stage IIIB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. - Chris Stoeckert, Helena Ellis - Stage IIIB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IIIB (AJCC 7th) @@ -128479,11 +139536,11 @@ realizes some 'host of immune response role' Stage IIIC (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. - Chris Stoeckert, Helena Ellis - Stage IIIC - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. + Chris Stoeckert, Helena Ellis + Stage IIIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IIIC (AJCC 7th) @@ -128495,11 +139552,11 @@ realizes some 'host of immune response role' Stage IVA (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. - Chris Stoeckert, Helena Ellis - Stage IVA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IVA (AJCC 7th) @@ -128511,11 +139568,11 @@ realizes some 'host of immune response role' Stage IVB (AJCC 7th) - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. - Chris Stoeckert, Helena Ellis - Stage IVB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB Stage IVB (AJCC 7th) @@ -128527,11 +139584,11 @@ realizes some 'host of immune response role' Stage IA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. - Chris Stoeckert, Helena Ellis - Stage IA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. + Chris Stoeckert, Helena Ellis + Stage IA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IA (FIGO) @@ -128543,11 +139600,11 @@ realizes some 'host of immune response role' Stage IA1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. - Chris Stoeckert, Helena Ellis - Stage IA1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IA1 (FIGO) @@ -128559,11 +139616,11 @@ realizes some 'host of immune response role' Stage IA2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. - Chris Stoeckert, Helena Ellis - Stage IA2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IA2 (FIGO) @@ -128575,11 +139632,11 @@ realizes some 'host of immune response role' Stage IB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA - Chris Stoeckert, Helena Ellis - Stage IB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA + Chris Stoeckert, Helena Ellis + Stage IB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IB (FIGO) @@ -128591,11 +139648,11 @@ realizes some 'host of immune response role' Stage IB1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IB1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IB1 (FIGO) @@ -128607,11 +139664,11 @@ realizes some 'host of immune response role' Stage IB2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IB2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IB2 (FIGO) @@ -128623,11 +139680,11 @@ realizes some 'host of immune response role' Stage IIA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. - Chris Stoeckert, Helena Ellis - Stage IIA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IIA (FIGO) @@ -128639,11 +139696,11 @@ realizes some 'host of immune response role' Stage IIA1 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IIA1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IIA1 (FIGO) @@ -128655,11 +139712,11 @@ realizes some 'host of immune response role' Stage IIA2 (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IIA2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IIA2 (FIGO) @@ -128671,11 +139728,11 @@ realizes some 'host of immune response role' Stage IIB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. - Chris Stoeckert, Helena Ellis - Stage IIB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IIB (FIGO) @@ -128687,11 +139744,11 @@ realizes some 'host of immune response role' Stage IIIA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. - Chris Stoeckert, Helena Ellis - Stage IIIA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IIIA (FIGO) @@ -128703,11 +139760,11 @@ realizes some 'host of immune response role' Stage IIIB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. - Chris Stoeckert, Helena Ellis - Stage IIIB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IIIB (FIGO) @@ -128719,11 +139776,11 @@ realizes some 'host of immune response role' Stage IVA (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. - Chris Stoeckert, Helena Ellis - Stage IVA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IVA (FIGO) @@ -128735,11 +139792,11 @@ realizes some 'host of immune response role' Stage IVB (FIGO) - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. - Chris Stoeckert, Helena Ellis - Stage IVB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB Stage IVB (FIGO) @@ -128751,11 +139808,11 @@ realizes some 'host of immune response role' Stage 1 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 1 (FIGO) @@ -128767,11 +139824,11 @@ realizes some 'host of immune response role' Stage 1A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 1A (FIGO) @@ -128783,11 +139840,11 @@ realizes some 'host of immune response role' Stage 1B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 1B (FIGO) @@ -128799,11 +139856,11 @@ realizes some 'host of immune response role' Stage 1C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 1C (FIGO) @@ -128815,11 +139872,11 @@ realizes some 'host of immune response role' Stage 2 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 2 (FIGO) @@ -128831,11 +139888,11 @@ realizes some 'host of immune response role' Stage 2A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 2A (FIGO) @@ -128847,11 +139904,11 @@ realizes some 'host of immune response role' Stage 2B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 2B (FIGO) @@ -128863,11 +139920,11 @@ realizes some 'host of immune response role' Stage 2C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 2C (FIGO) @@ -128879,11 +139936,11 @@ realizes some 'host of immune response role' Stage 3 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). - Chris Stoeckert, Helena Ellis - Stage 3 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). + Chris Stoeckert, Helena Ellis + Stage 3 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 3 (FIGO) @@ -128895,11 +139952,11 @@ realizes some 'host of immune response role' Stage 3A (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . - Chris Stoeckert, Helena Ellis - Stage 3A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 3A (FIGO) @@ -128911,11 +139968,11 @@ realizes some 'host of immune response role' Stage 3B (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . - Chris Stoeckert, Helena Ellis - Stage 3B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 3B (FIGO) @@ -128927,11 +139984,11 @@ realizes some 'host of immune response role' Stage 3C (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). - Chris Stoeckert, Helena Ellis - Stage 3C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). + Chris Stoeckert, Helena Ellis + Stage 3C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 3C (FIGO) @@ -128943,11 +140000,11 @@ realizes some 'host of immune response role' Stage 4 (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. - Chris Stoeckert, Helena Ellis - Stage 4 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + Chris Stoeckert, Helena Ellis + Stage 4 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage 4 (FIGO) @@ -128959,11 +140016,11 @@ realizes some 'host of immune response role' Stage Unknown (FIGO) - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). - Chris Stoeckert, Helena Ellis - Stage Unknown - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). + Chris Stoeckert, Helena Ellis + Stage Unknown + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB Stage Unknown (FIGO) @@ -128975,10 +140032,10 @@ realizes some 'host of immune response role' 3: symptomatic in bed more than 50% of the day but not bed ridden - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 3: symptomatic in bed more than 50% of the day but not bed ridden @@ -128990,10 +140047,10 @@ realizes some 'host of immune response role' 2: symptomatic but in bed less than 50% of the day - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 2: symptomatic but in bed less than 50% of the day @@ -129005,10 +140062,10 @@ realizes some 'host of immune response role' 4: bed ridden - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 4: bed ridden @@ -129020,10 +140077,10 @@ realizes some 'host of immune response role' 0: asymptomatic - An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 0: asymptomatic @@ -129035,10 +140092,10 @@ realizes some 'host of immune response role' 1: symptomatic but fully ambulatory - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 1: symptomatic but fully ambulatory @@ -129050,10 +140107,10 @@ realizes some 'host of immune response role' 100: asymptomatic - A Karnofsky score vaue specification indicating that a patient is asymptomatic. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A Karnofsky score vaue specification indicating that a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 100: asymptomatic @@ -129065,10 +140122,10 @@ realizes some 'host of immune response role' 80-90: symptomatic but fully ambulatory - A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 80-90: symptomatic but fully ambulatory @@ -129080,10 +140137,10 @@ realizes some 'host of immune response role' 60-70: symptomatic but in bed less than 50% of the day - A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 60-70: symptomatic but in bed less than 50% of the day @@ -129095,10 +140152,10 @@ realizes some 'host of immune response role' 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden - A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB + A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden @@ -129108,12 +140165,12 @@ realizes some 'host of immune response role' - Oxford Nanopore Technologies + Oxford Nanopore Technologies - An organization that is developing and selling nanopore sequencing products and is based in the UK. - James A. Overton - https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies - Oxford Nanopore Technologies + An organization that is developing and selling nanopore sequencing products and is based in the UK. + James A. Overton + https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies + Oxford Nanopore Technologies @@ -129122,12 +140179,12 @@ realizes some 'host of immune response role' - BioGents + BioGents - An organization that manufactures mosquito traps and other mosquito control products. - John Judkins - WEB:https://eu.biogents.com/about-biogents/ - BioGents + An organization that manufactures mosquito traps and other mosquito control products. + John Judkins + WEB:https://eu.biogents.com/about-biogents/ + BioGents @@ -129205,11 +140262,11 @@ binary, and takes no temporal argument. - meter - A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. - m + meter + A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. + m - meter + meter @@ -129218,11 +140275,11 @@ binary, and takes no temporal argument. - kilogram - A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. - kg + kilogram + A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. + kg - kilogram + kilogram @@ -129231,12 +140288,12 @@ binary, and takes no temporal argument. - second - A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. - s - sec + second + A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + s + sec - second + second @@ -129245,11 +140302,11 @@ binary, and takes no temporal argument. - centimeter - A length unit which is equal to one hundredth of a meter or 10^[-2] m. - cm + centimeter + A length unit which is equal to one hundredth of a meter or 10^[-2] m. + cm - centimeter + centimeter @@ -129258,11 +140315,11 @@ binary, and takes no temporal argument. - millimeter - A length unit which is equal to one thousandth of a meter or 10^[-3] m. - mm + millimeter + A length unit which is equal to one thousandth of a meter or 10^[-3] m. + mm - millimeter + millimeter @@ -129271,11 +140328,11 @@ binary, and takes no temporal argument. - micrometer - A length unit which is equal to one millionth of a meter or 10^[-6] m. - um + micrometer + A length unit which is equal to one millionth of a meter or 10^[-6] m. + um - micrometer + micrometer @@ -129284,11 +140341,11 @@ binary, and takes no temporal argument. - nanometer - A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. - nm + nanometer + A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. + nm - nanometer + nanometer @@ -129297,10 +140354,10 @@ binary, and takes no temporal argument. - angstrom - A length unit which is equal to 10 [-10] m. + angstrom + A length unit which is equal to 10 [-10] m. - angstrom + angstrom @@ -129309,11 +140366,11 @@ binary, and takes no temporal argument. - gram - A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. - g + gram + A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. + g - gram + gram @@ -129322,11 +140379,11 @@ binary, and takes no temporal argument. - milligram - A mass unit which is equal to one thousandth of a gram or 10^[-3] g. - mg + milligram + A mass unit which is equal to one thousandth of a gram or 10^[-3] g. + mg - milligram + milligram @@ -129335,11 +140392,11 @@ binary, and takes no temporal argument. - microgram - A mass unit which is equal to one millionth of a gram or 10^[-6] g. - ug + microgram + A mass unit which is equal to one millionth of a gram or 10^[-6] g. + ug - microgram + microgram @@ -129348,11 +140405,11 @@ binary, and takes no temporal argument. - nanogram - A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. - ng + nanogram + A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. + ng - nanogram + nanogram @@ -129361,11 +140418,11 @@ binary, and takes no temporal argument. - picogram - A mass unit which is equal to 10^[-12] g. - pg + picogram + A mass unit which is equal to 10^[-12] g. + pg - picogram + picogram @@ -129374,12 +140431,12 @@ binary, and takes no temporal argument. - degree Celsius - A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. - C - degree C + degree Celsius + A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. + C + degree C - degree Celsius + degree Celsius @@ -129388,11 +140445,11 @@ binary, and takes no temporal argument. - minute - A time unit which is equal to 60 seconds. - min + minute + A time unit which is equal to 60 seconds. + min - minute + minute @@ -129401,12 +140458,12 @@ binary, and takes no temporal argument. - hour - A time unit which is equal to 3600 seconds or 60 minutes. - h - hr + hour + A time unit which is equal to 3600 seconds or 60 minutes. + h + hr - hour + hour @@ -129415,10 +140472,10 @@ binary, and takes no temporal argument. - day - A time unit which is equal to 24 hours. + day + A time unit which is equal to 24 hours. - day + day @@ -129427,10 +140484,10 @@ binary, and takes no temporal argument. - week - A time unit which is equal to 7 days. + week + A time unit which is equal to 7 days. - week + week @@ -129439,10 +140496,10 @@ binary, and takes no temporal argument. - month - A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. + month + A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. - month + month @@ -129451,10 +140508,10 @@ binary, and takes no temporal argument. - year - A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. + year + A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. - year + year @@ -129463,11 +140520,11 @@ binary, and takes no temporal argument. - micromole - A substance unit equal to a millionth of a mol or 10^[-6] mol. - umol + micromole + A substance unit equal to a millionth of a mol or 10^[-6] mol. + umol - micromole + micromole @@ -129476,11 +140533,11 @@ binary, and takes no temporal argument. - nanomole - A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. - nmol + nanomole + A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. + nmol - nanomole + nanomole @@ -129489,11 +140546,11 @@ binary, and takes no temporal argument. - picomole - A substance unit equal to 10^[-12] mol. - pmol + picomole + A substance unit equal to 10^[-12] mol. + pmol - picomole + picomole @@ -129502,11 +140559,11 @@ binary, and takes no temporal argument. - molar - A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). - M + molar + A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). + M - molar + molar @@ -129515,11 +140572,11 @@ binary, and takes no temporal argument. - millimolar - A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. - mM + millimolar + A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. + mM - millimolar + millimolar @@ -129528,11 +140585,11 @@ binary, and takes no temporal argument. - micromolar - A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. - uM + micromolar + A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. + uM - micromolar + micromolar @@ -129541,11 +140598,11 @@ binary, and takes no temporal argument. - nanomolar - A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. - nM + nanomolar + A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. + nM - nanomolar + nanomolar @@ -129554,11 +140611,11 @@ binary, and takes no temporal argument. - picomolar - A unit of molarity which is equal to 10^[-12] M. - pM + picomolar + A unit of molarity which is equal to 10^[-12] M. + pM - picomolar + picomolar @@ -129567,11 +140624,11 @@ binary, and takes no temporal argument. - cubic centimeter - A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. - cc + cubic centimeter + A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. + cc - cubic centimeter + cubic centimeter @@ -129580,11 +140637,11 @@ binary, and takes no temporal argument. - milliliter - A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. - ml + milliliter + A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. + ml - milliliter + milliliter @@ -129593,11 +140650,11 @@ binary, and takes no temporal argument. - liter - A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. - L + liter + A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. + L - liter + liter @@ -129606,10 +140663,10 @@ binary, and takes no temporal argument. - cubic decimeter - A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. + cubic decimeter + A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. - cubic decimeter + cubic decimeter @@ -129618,11 +140675,11 @@ binary, and takes no temporal argument. - microliter - A volume unit which is equal to one millionth of a liter or 10^[-6] L. - ul + microliter + A volume unit which is equal to one millionth of a liter or 10^[-6] L. + ul - microliter + microliter @@ -129631,11 +140688,11 @@ binary, and takes no temporal argument. - nanoliter - A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. - nl + nanoliter + A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. + nl - nanoliter + nanoliter @@ -129644,11 +140701,11 @@ binary, and takes no temporal argument. - picoliter - A volume unit which is equal to 10^[-12] L. - pl + picoliter + A volume unit which is equal to 10^[-12] L. + pl - picoliter + picoliter @@ -129657,10 +140714,10 @@ binary, and takes no temporal argument. - hertz - A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. + hertz + A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. - hertz + hertz @@ -129669,12 +140726,12 @@ binary, and takes no temporal argument. - mass percentage - A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. - % w/w - percent weight pr weight + mass percentage + A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. + % w/w + percent weight pr weight - mass percentage + mass percentage @@ -129683,12 +140740,12 @@ binary, and takes no temporal argument. - mass volume percentage - A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. - % w/v - percent vol per vol + mass volume percentage + A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. + % w/v + percent vol per vol - mass volume percentage + mass volume percentage @@ -129697,12 +140754,12 @@ binary, and takes no temporal argument. - volume percentage - A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. - % v/v - percent vol per vol + volume percentage + A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. + % v/v + percent vol per vol - volume percentage + volume percentage @@ -129711,12 +140768,12 @@ binary, and takes no temporal argument. - gram per liter - A mass unit density which is equal to mass of an object in grams divided by the volume in liters. - g per L - g/L + gram per liter + A mass unit density which is equal to mass of an object in grams divided by the volume in liters. + g per L + g/L - gram per liter + gram per liter @@ -129725,12 +140782,12 @@ binary, and takes no temporal argument. - milligram per milliliter - A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. - mg per ml - mg/ml + milligram per milliliter + A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. + mg per ml + mg/ml - milligram per milliliter + milligram per milliliter @@ -129739,10 +140796,10 @@ binary, and takes no temporal argument. - degree Fahrenheit - A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. + degree Fahrenheit + A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. - degree Fahrenheit + degree Fahrenheit @@ -129751,10 +140808,10 @@ binary, and takes no temporal argument. - pH - A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). + pH + A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). - pH + pH @@ -129763,12 +140820,12 @@ binary, and takes no temporal argument. - milliliter per liter - A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. - ml per L - ml/l + milliliter per liter + A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. + ml per L + ml/l - milliliter per liter + milliliter per liter @@ -129777,11 +140834,11 @@ binary, and takes no temporal argument. - gram per deciliter - A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. - g/dl + gram per deciliter + A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. + g/dl - gram per deciliter + gram per deciliter @@ -129790,10 +140847,10 @@ binary, and takes no temporal argument. - colony forming unit per volume - A concentration unit which a measure of viable bacterial numbers in a given volume. + colony forming unit per volume + A concentration unit which a measure of viable bacterial numbers in a given volume. - colony forming unit per volume + colony forming unit per volume @@ -129802,10 +140859,10 @@ binary, and takes no temporal argument. - microliters per minute - A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. + microliters per minute + A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. - microliters per minute + microliters per minute @@ -129814,10 +140871,10 @@ binary, and takes no temporal argument. - count per nanomolar second - A rate unit which is equal to one over one nanomolar second. + count per nanomolar second + A rate unit which is equal to one over one nanomolar second. - count per nanomolar second + count per nanomolar second @@ -129826,10 +140883,10 @@ binary, and takes no temporal argument. - count per molar second - A rate unit which is equal to one over one molar second. + count per molar second + A rate unit which is equal to one over one molar second. - count per molar second + count per molar second @@ -129838,10 +140895,10 @@ binary, and takes no temporal argument. - count per nanomolar - A rate unit which is equal to one over one nanomolar. + count per nanomolar + A rate unit which is equal to one over one nanomolar. - count per nanomolar + count per nanomolar @@ -129850,10 +140907,10 @@ binary, and takes no temporal argument. - count per molar - A rate unit which is equal to one over one molar. + count per molar + A rate unit which is equal to one over one molar. - count per molar + count per molar @@ -129862,12 +140919,12 @@ binary, and takes no temporal argument. - microgram per liter - A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. - ng/ml - ug/L + microgram per liter + A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. + ng/ml + ug/L - microgram per liter + microgram per liter @@ -129918,8 +140975,8 @@ binary, and takes no temporal argument. - A reference to a place on the Earth, by its name or by its geographical location. - geographic location + A reference to a place on the Earth, by its name or by its geographical location. + geographic location diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index d66b86a3..30b20497 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2021-08-18 + 2022-01-03 @@ -165,9 +165,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -194,9 +194,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -617,12 +617,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which is_supported_by_data - The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. + The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process + The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI - Philly 2011 workshop + Philly 2011 workshop is_supported_by_data @@ -639,16 +639,16 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has_specified_input has_specified_input - has_specified_input see is_input_of example_of_usage - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + The inverse property of is_specified_input_of + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot has_specified_input @@ -660,12 +660,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_specified_input_of + is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_input_of @@ -682,14 +682,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has_specified_output has_specified_output - has_specified_output - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + The inverse property of is_specified_output_of PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot has_specified_output @@ -706,12 +706,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + is_specified_output_of is_specified_output_of - is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_output_of @@ -724,14 +724,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - achieves_planned_objective - A cell sorting process achieves the objective specification 'material separation objective' + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. - BP, AR, PPPB branch - PPPB branch derived - modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - achieves_planned_objective + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + achieves_planned_objective @@ -740,13 +740,13 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - has grain + has grain - the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. + the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg - PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 - has grain + PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 + has grain @@ -755,13 +755,13 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - provisions + provisions - A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use + A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use 5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship. - GROUP: Relations branch + GROUP: Relations branch supplies - provisions + provisions @@ -778,14 +778,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - has_supplier + has_supplier - A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. - PERSON: Alan Rutternberg - PERSON: Cristian Cocos - PERSON: Frank Gibson - PERSON: Melanie Courtot - has_supplier + A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. + PERSON: Alan Rutternberg + PERSON: Cristian Cocos + PERSON: Frank Gibson + PERSON: Melanie Courtot + has_supplier @@ -795,12 +795,12 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - objective_achieved_by + objective_achieved_by - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - objective_achieved_by + objective_achieved_by @@ -818,17 +818,17 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is member of organization + is member of organization - Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. - 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population - JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. - Person:Alan Ruttenberg - Person:Helen Parkinson - Person:Alan Ruttenberg - Person:Helen Parkinson - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - is member of organization + Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. + 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population + JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. + Person:Alan Ruttenberg + Person:Helen Parkinson + Person:Alan Ruttenberg + Person:Helen Parkinson + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + is member of organization @@ -847,10 +847,10 @@ Werner suggests a solution based on "Magnitudes" a proposal for which has organization member - Relating an organization to a legal person or organization. - See tracker: + Relating an organization to a legal person or organization. + See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 - Person: Jie Zheng + Person: Jie Zheng has organization member @@ -1034,7 +1034,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - derives from + derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) @@ -1568,10 +1568,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + peptide + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. - peptide + peptide @@ -1580,11 +1580,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - molecular entity + molecular entity @@ -1593,10 +1593,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + nucleic acid + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. - nucleic acid + nucleic acid @@ -1605,10 +1605,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - ribonucleic acid - High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. + ribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. - ribonucleic acid + ribonucleic acid @@ -1617,11 +1617,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - macromolecule - A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + macromolecule + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer - macromolecule + macromolecule @@ -1630,13 +1630,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + cell cell - cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + cell cell - cell @@ -1664,10 +1664,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cultured cell - A cell in vitro that is or has been maintained or propagated as part of a cell culture. + cultured cell + A cell in vitro that is or has been maintained or propagated as part of a cell culture. - cultured cell + cultured cell @@ -1676,11 +1676,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell - A lymphocyte of B lineage that is capable of B cell mediated immunity. + B cell + A lymphocyte of B lineage that is capable of B cell mediated immunity. A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. - B cell + B cell @@ -1689,10 +1689,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lymphocyte - A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. + lymphocyte + A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - lymphocyte + lymphocyte @@ -1708,10 +1708,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - experimentally modified cell in vitro - A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. + experimentally modified cell in vitro + A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. - experimentally modified cell in vitro + experimentally modified cell in vitro @@ -1720,10 +1720,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mononuclear cell - A leukocyte with a single non-segmented nucleus in the mature form. + mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form. - mononuclear cell + mononuclear cell @@ -1732,11 +1732,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - environmental material - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. + environmental material + A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. CS20 - environmental material + environmental material @@ -1753,10 +1753,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - molecular_function - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular_function + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. - molecular_function + molecular_function @@ -1765,10 +1765,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - catalytic activity - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + catalytic activity + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - catalytic activity + catalytic activity @@ -1777,10 +1777,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - RNA-directed DNA polymerase activity - Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. + RNA-directed DNA polymerase activity + Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. - RNA-directed DNA polymerase activity + RNA-directed DNA polymerase activity @@ -1790,10 +1790,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological_process + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - biological_process + biological_process @@ -1808,12 +1808,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - protein-containing complex + protein-containing complex A ribosome is a protein complex. - A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein complex - protein-containing complex + protein-containing complex @@ -2536,9 +2536,9 @@ Request that IAO either clarify these or change definitions not to use them - Viruses + Viruses - Viruses + Viruses @@ -2547,10 +2547,10 @@ Request that IAO either clarify these or change definitions not to use them - Euteleostomi - bony vertebrates + Euteleostomi + bony vertebrates - Euteleostomi + Euteleostomi @@ -2559,10 +2559,10 @@ Request that IAO either clarify these or change definitions not to use them - Bacteria - eubacteria + Bacteria + eubacteria - Bacteria + Bacteria @@ -2571,9 +2571,9 @@ Request that IAO either clarify these or change definitions not to use them - Archaea + Archaea - Archaea + Archaea @@ -2582,11 +2582,11 @@ Request that IAO either clarify these or change definitions not to use them - Eukaryota - eucaryotes - eukaryotes + Eukaryota + eucaryotes + eukaryotes - Eukaryota + Eukaryota @@ -2595,9 +2595,9 @@ Request that IAO either clarify these or change definitions not to use them - Euarchontoglires + Euarchontoglires - Euarchontoglires + Euarchontoglires @@ -2606,10 +2606,10 @@ Request that IAO either clarify these or change definitions not to use them - Tetrapoda - tetrapods + Tetrapoda + tetrapods - Tetrapoda + Tetrapoda @@ -2618,10 +2618,10 @@ Request that IAO either clarify these or change definitions not to use them - Amniota - amniotes + Amniota + amniotes - Amniota + Amniota @@ -2630,9 +2630,9 @@ Request that IAO either clarify these or change definitions not to use them - Opisthokonta + Opisthokonta - Opisthokonta + Opisthokonta @@ -2641,9 +2641,9 @@ Request that IAO either clarify these or change definitions not to use them - Bilateria + Bilateria - Bilateria + Bilateria @@ -2652,10 +2652,10 @@ Request that IAO either clarify these or change definitions not to use them - Mammalia - mammals + Mammalia + mammals - Mammalia + Mammalia @@ -2664,11 +2664,11 @@ Request that IAO either clarify these or change definitions not to use them - Vertebrata <vertebrates> - Vertebrata - vertebrates + Vertebrata <vertebrates> + Vertebrata + vertebrates - Vertebrata <vertebrates> + Vertebrata <vertebrates> @@ -2677,12 +2677,12 @@ Request that IAO either clarify these or change definitions not to use them - Homo sapiens - human - human being - man + Homo sapiens + human + human being + man - Homo sapiens + Homo sapiens @@ -2702,17 +2702,17 @@ Request that IAO either clarify these or change definitions not to use them + planned process planned process - planned process - Injecting mice with a vaccine in order to test its efficacy + Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process @@ -2797,12 +2797,12 @@ objectives is a planned process. investigation - Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation + Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived - Could add specific objective specification + Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS @@ -2833,9 +2833,9 @@ editor = PRS a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") - GROUP: Role Branch - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role @@ -2845,15 +2845,15 @@ editor = PRS - reporting party role - Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. + reporting party role + Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm a study personnel role played by a party who reports the outcome of a study component - MO:submitter mapped to this term. So, alternative term 'submitter' was added. + MO:submitter mapped to this term. So, alternative term 'submitter' was added. Jennifer Fostel - reporting party - submitter + reporting party + submitter OBI reporting party role @@ -2921,7 +2921,7 @@ editor = PRS assay - Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. @@ -2959,11 +2959,11 @@ editor = PRS - culture medium + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 - a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. - changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 + a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. + changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI @@ -2994,15 +2994,15 @@ Modification made by JZ. - material processing - A cell lysis, production of a cloning vector, creating a buffer. + material processing + A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca Serra + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing @@ -3014,12 +3014,12 @@ Modification made by JZ. - responsible party role + responsible party role he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study Person: Jennifer Fostel - responsible party + responsible party OBI responsible party role @@ -3030,11 +3030,11 @@ Modification made by JZ. - principal investigator role + principal investigator role a responsible party role played by a person responsible for the overall conduct of a study Person: Jennifer Fostel - principal investigator + principal investigator CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) principal investigator role @@ -3061,20 +3061,20 @@ Modification made by JZ. - specimen role - liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation - 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. - GROUP: Role Branch - OBI + GROUP: Role Branch + OBI specimen role @@ -3121,18 +3121,18 @@ specimen can later be subject. - investigation agent role + investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. - Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. + Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch - investigator + investigator OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) - investigation agent role + investigation agent role @@ -3172,11 +3172,11 @@ This leads to my proposal: We define organization through the statements 1 - current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - PERSON: Susanna Sansone - GROUP: OBI + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI organization @@ -3213,13 +3213,13 @@ for now. - interpreting data - Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. + interpreting data + Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - Bjoern Peters + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + Bjoern Peters drawing a conclusion based on data @@ -3240,14 +3240,14 @@ for now. - planning - The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. + planning + The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification - 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. - Bjoern Peters - Bjoern Peters - Plans and Planned Processes Branch + 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. + Bjoern Peters + Bjoern Peters + Plans and Planned Processes Branch planning @@ -3277,8 +3277,8 @@ for now. enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) - person:Melanie Courtot - group:OBI + person:Melanie Courtot + group:OBI reverse transcriptase @@ -3298,9 +3298,9 @@ activity) Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra extracted material - GROUP: OBI Biomatrial Branch + GROUP: OBI Biomatrial Branch extract @@ -3314,9 +3314,9 @@ activity) A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi averaging objective @@ -3365,10 +3365,10 @@ activity) (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) - MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything + MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. - person: Melanie Courtot - GROUP:OBI + person: Melanie Courtot + GROUP:OBI enzyme @@ -3378,12 +3378,12 @@ that has_part some material entity is a material entity. If we add as equivalent - assay objective - the objective to determine the weight of a mouse. + assay objective + the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) - PPPB branch - PPPB branch + PPPB branch + PPPB branch assay objective @@ -3411,13 +3411,13 @@ that has_part some material entity is a material entity. If we add as equivalent measure function - A glucometer measures blood glucose concentration, the glucometer has a measure function. + A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. - PERSON: Daniel Schober - PERSON: Helen Parkinson - PERSON: Melanie Courtot - PERSON:Frank Gibson + PERSON: Daniel Schober + PERSON: Helen Parkinson + PERSON: Melanie Courtot + PERSON:Frank Gibson measure function @@ -3427,17 +3427,17 @@ that has_part some material entity is a material entity. If we add as equivalent - material transformation objective - The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra artifact creation objective - GROUP: OBI PlanAndPlannedProcess Branch + GROUP: OBI PlanAndPlannedProcess Branch material transformation objective @@ -3463,15 +3463,15 @@ that has_part some material entity is a material entity. If we add as equivalent - study design execution - injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. + study design execution + injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. - a planned process that carries out a study design - removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. - branch derived - 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. + a planned process that carries out a study design + removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. + branch derived + 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution + study design execution @@ -3488,13 +3488,13 @@ that has_part some material entity is a material entity. If we add as equivalent - material separation objective - The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. + material separation objective + The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. - is an objective to transform a material entity into spatially separated components. - PPPB branch - PPPB branch - material separation objective + is an objective to transform a material entity into spatially separated components. + PPPB branch + PPPB branch + material separation objective @@ -3529,16 +3529,16 @@ that has_part some material entity is a material entity. If we add as equivalent specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation - A planned process with the objective of collecting a specimen. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ - Bjoern Peters + Bjoern Peters specimen collection - 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession - 6/9/09: used at workshop + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop specimen collection process @@ -3569,12 +3569,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - sample from organism + sample from organism - a material obtained from an organism in order to be a representative of the whole - 5/29: This is a helper class for now - we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. - sample from organism + a material obtained from an organism in order to be a representative of the whole + 5/29: This is a helper class for now + we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. + sample from organism @@ -3584,11 +3584,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - portioning objective - The objective to obtain multiple aliquots of an enzyme preparation. + portioning objective + The objective to obtain multiple aliquots of an enzyme preparation. - A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. - portioning objective + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. + portioning objective @@ -3603,12 +3603,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - average value + average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - arithmetic mean + PERSON: James Malone + PERSON: Monnie McGee + arithmetic mean average value @@ -3618,12 +3618,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - separation into different composition objective - The objective to obtain cells contained in a sample of blood. + separation into different composition objective + The objective to obtain cells contained in a sample of blood. - A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). - We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives - separation into different composition objective + A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). + We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives + separation into different composition objective @@ -3633,11 +3633,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective - The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. - Bjoern Peters - Bjoern Peters + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters specimen collection objective @@ -3647,12 +3647,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - material sample role - a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. + material sample role + a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. - A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. - 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. - material sample role + A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. + 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. + material sample role @@ -3676,12 +3676,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - material sampling process + material sampling process - A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity + A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity sample collection sampling - material sampling process + material sampling process @@ -3701,13 +3701,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - material sample - blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. + material sample + blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. - A material entity that has the material sample role - OBI: workshop - sample population - material sample + A material entity that has the material sample role + OBI: workshop + sample population + material sample @@ -3716,12 +3716,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - material maintenance objective + material maintenance objective - An objective specification maintains some or all of the qualities of a material over time. - PERSON: Bjoern Peters - PERSON: Bjoern Peters - material maintenance objective + An objective specification maintains some or all of the qualities of a material over time. + PERSON: Bjoern Peters + PERSON: Bjoern Peters + material maintenance objective @@ -3741,13 +3741,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - measurement device - A ruler, a microarray scanner, a Geiger counter. + measurement device + A ruler, a microarray scanner, a Geiger counter. - A device in which a measure function inheres. - GROUP:OBI Philly workshop - OBI - measurement device + A device in which a measure function inheres. + GROUP:OBI Philly workshop + OBI + measurement device @@ -3762,10 +3762,10 @@ http://sourceforge.net/p/obi/obi-terms/716/ - material maintenance + material maintenance - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time - material maintenance + a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + material maintenance @@ -3785,11 +3785,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ - primary structure of RNA molecule + primary structure of RNA molecule - The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together - Person:Bjoern Peters - primary structure of RNA molecule + The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together + Person:Bjoern Peters + primary structure of RNA molecule @@ -3798,13 +3798,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - sequence feature annotation + sequence feature annotation - Information about a sequence region - Bjoern Peters - Bjoern Peters - place holder for sequence ontology term - sequence feature annotation + Information about a sequence region + Bjoern Peters + Bjoern Peters + place holder for sequence ontology term + sequence feature annotation @@ -3819,7 +3819,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - infectious agent + infectious agent is a material entity bearing the disposition to infect an organism IEDB @@ -3847,13 +3847,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - service consumer role - A biologist who uses a sequencing services fulfills the role of a service consumer + service consumer role + A biologist who uses a sequencing services fulfills the role of a service consumer - a role which inheres in a person who uses a service - Person:Helen Parkinson - OBI - service consumer role + a role which inheres in a person who uses a service + Person:Helen Parkinson + OBI + service consumer role @@ -3881,12 +3881,12 @@ http://sourceforge.net/p/obi/obi-terms/716/ - service provider role - Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. + service provider role + Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. - is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person - PERSON:Helen Parkinson - service provider role + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + PERSON:Helen Parkinson + service provider role @@ -3904,15 +3904,15 @@ http://sourceforge.net/p/obi/obi-terms/716/ - processed specimen + processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. - A specimen that has been intentionally physically modified. - Bjoern Peters - Bjoern Peters + A specimen that has been intentionally physically modified. + Bjoern Peters + Bjoern Peters A tissue sample that has been sliced and stained for a histology study. - processed specimen + processed specimen @@ -3933,12 +3933,12 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: @@ -3949,10 +3949,10 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device @@ -3961,14 +3961,14 @@ In the examples above, a reagent is an operational component of a device, but th - fresh specimen - a liver freshly removed from a rat + fresh specimen + a liver freshly removed from a rat - a specimen that is output of a specimen creation process used for an investigation without storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_730 fresh_sample - fresh specimen + a specimen that is output of a specimen creation process used for an investigation without storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_730 fresh_sample + fresh specimen @@ -3988,13 +3988,13 @@ In the examples above, a reagent is an operational component of a device, but th - sequence data - example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. + sequence data + example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. - Person:Chris Stoeckert - GROUP: OBI + Person:Chris Stoeckert + GROUP: OBI sequence data @@ -4025,12 +4025,12 @@ In the examples above, a reagent is an operational component of a device, but th - nucleic acid extract + nucleic acid extract - An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. - PERSON: Jie Zheng - UPenn Group - nucleic acid extract + An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + PERSON: Jie Zheng + UPenn Group + nucleic acid extract @@ -4045,12 +4045,12 @@ In the examples above, a reagent is an operational component of a device, but th - nucleic acid sequencer + nucleic acid sequencer - An device that is used to determine the order of nucleotides in nucleic acid sequences. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - nucleic acid sequencer + An device that is used to determine the order of nucleotides in nucleic acid sequences. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + nucleic acid sequencer @@ -4065,12 +4065,12 @@ In the examples above, a reagent is an operational component of a device, but th - protein sequencer + protein sequencer - An device that is used to determine the order of amino acids in protein sequences. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - protein sequencer + An device that is used to determine the order of amino acids in protein sequences. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + protein sequencer @@ -4088,7 +4088,7 @@ In the examples above, a reagent is an operational component of a device, but th individual organism identifier a CRID symbol used to distinguish one individual organism from another. - PERSON: Chris Stoeckert, Jie Zheng + PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual CS1 individual organism identifier @@ -4108,18 +4108,18 @@ In the examples above, a reagent is an operational component of a device, but th age measurement datum - A time measurement datum that is the result of measurement of age of an organism - note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. + A time measurement datum that is the result of measurement of age of an organism + note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage - PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng - MO_178 Age - In MageTab file, we use + PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng + MO_178 Age + In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class - discussed on Nov 15, dev call + discussed on Nov 15, dev call All subtype will be defined by textual definition now. CS6 age measurement datum @@ -4156,13 +4156,13 @@ All subtype will be defined by textual definition now. - service - providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony + service + providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony - A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. - Carlo; Matt - OBI workshop San Diego 2011 - service + A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. + Carlo; Matt + OBI workshop San Diego 2011 + service @@ -4189,9 +4189,9 @@ All subtype will be defined by textual definition now. specimen with known storage state - A specimen for which it is known whether it has been subjected to storage of a specified type. - PERSON: Chris Stoeckert, Jie Zheng - MO_95 BiosourceType + A specimen for which it is known whether it has been subjected to storage of a specified type. + PERSON: Chris Stoeckert, Jie Zheng + MO_95 BiosourceType specimen with known storage state @@ -4224,10 +4224,10 @@ All subtype will be defined by textual definition now. specimen from organism - A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). - PERSON: Chris Stoeckert, Jie Zheng + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + PERSON: Chris Stoeckert, Jie Zheng tissue specimen - MO_954 organism_part + MO_954 organism_part CS16 specimen from organism @@ -4249,15 +4249,15 @@ All subtype will be defined by textual definition now. - material maintenance service - model organism colony maintanance + material maintenance service + model organism colony maintanance - A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. - material maintenance service + A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. + material maintenance service @@ -4306,14 +4306,14 @@ All subtype will be defined by textual definition now. - material service - A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization + material service + A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization - A service which has a material entity as specified input and/or specified output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material service + A service which has a material entity as specified input and/or specified output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material service @@ -4333,14 +4333,14 @@ All subtype will be defined by textual definition now. - material analysis service - Services performing DNA sequencing or Cell Analysis + material analysis service + Services performing DNA sequencing or Cell Analysis - A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - material analysis service + A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + material analysis service @@ -4360,14 +4360,14 @@ All subtype will be defined by textual definition now. - material storage service - A service that offers liquid nitrogen stroage. + material storage service + A service that offers liquid nitrogen stroage. - A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - material storage service + A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + material storage service @@ -4623,10 +4623,10 @@ All subtype will be defined by textual definition now. organism identification assay - An assay that identifies the organism species in a specimen. - Chris Stoeckert - Jie Zheng - NIAID GSCID-BRC metadata working group + An assay that identifies the organism species in a specimen. + Chris Stoeckert + Jie Zheng + NIAID GSCID-BRC metadata working group CS21 organism identification assay @@ -4767,13 +4767,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 contact representative role - A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. + A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 - Person: Chris Stoeckert + Person: Chris Stoeckert NIAID GSCID-BRC contact representative role @@ -5698,10 +5698,10 @@ The following are NOT conclusions based on data: data themselves; results from p - cell freezing medium + cell freezing medium - A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. - PERSON: Matthew Brush + A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. + PERSON: Matthew Brush cell freezing medium @@ -5923,11 +5923,11 @@ http://vivoweb.org/ontology/core#FundingOrganization cytometry assay - An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. + An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. - An assay that counts and/or measures characteristics of cells. - IEDB - IEDB + An assay that counts and/or measures characteristics of cells. + IEDB + IEDB cytometry assay @@ -6020,9 +6020,9 @@ http://vivoweb.org/ontology/core#FundingOrganization lymphocyte assay - A cytometry assay that measures the abundance and/or characteristics of lymphocytes - James A. Overton, ORCID:0000-0001-5139-5572 - OBI + A cytometry assay that measures the abundance and/or characteristics of lymphocytes + James A. Overton, ORCID:0000-0001-5139-5572 + OBI lymphocyte assay @@ -6060,8 +6060,8 @@ http://vivoweb.org/ontology/core#FundingOrganization PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch Epstein Barr virus transformed B cell @@ -6088,11 +6088,11 @@ http://vivoweb.org/ontology/core#FundingOrganization virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism CS3 CS4 @@ -6117,12 +6117,12 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - PERSON: James Malone - PERSON: Philippe Rocca-Serra + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch CS2 specimen @@ -6152,18 +6152,18 @@ This issue is outside the scope of OBI. - cultured cell population + cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). - A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. + A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. - PERSON:Matthew Brush + PERSON:Matthew Brush cell culture sample - PERSON:Matthew Brush - The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. - cultured cell population + PERSON:Matthew Brush + The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. + cultured cell population @@ -6206,14 +6206,14 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard @@ -6263,7 +6263,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from averaging data transformation An averaging data transformation is a data transformation that has objective averaging. - James Malone + James Malone PERSON: James Malone averaging data transformation @@ -6280,14 +6280,14 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - extraction - nucleic acid extraction using phenol chloroform + extraction + nucleic acid extraction using phenol chloroform - A material separation in which a desired component of an input material is separated from the remainder + A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. - Person:Bjoern Peters - Philippe Rocca-Serra + Person:Bjoern Peters + Philippe Rocca-Serra extraction @@ -6309,12 +6309,12 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - storage + storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch storage @@ -6330,13 +6330,13 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - DNA sequencer - ABI 377 DNA Sequencer, ABI 310 DNA Sequencer + DNA sequencer + ABI 377 DNA Sequencer, ABI 310 DNA Sequencer - A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. - Trish Whetzel - MO - DNA sequencer + A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. + Trish Whetzel + MO + DNA sequencer @@ -6354,9 +6354,9 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. - PERSON: Chris Stoeckert + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. @@ -6630,11 +6630,11 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from sequencing assay - The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template + The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template - An assay the uses chemical or biochemical means to infer the sequence of a biomaterial - PlanAndPlannedProcess Branch - OBI branch derived + An assay the uses chemical or biochemical means to infer the sequence of a biomaterial + PlanAndPlannedProcess Branch + OBI branch derived SA4 sequencing assay @@ -6694,7 +6694,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - infection process + infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB @@ -6714,7 +6714,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - disposition to infect an organism + disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB @@ -6728,7 +6728,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - pathologic process + pathologic process abnormal, harmful processes caused by or associated with a disease IEDB @@ -6763,7 +6763,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from disease course The totality of all processes through which a given disease instance is realized. - replace 'OBI:occurrence of disease', need to add logical definition + replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease @@ -6784,10 +6784,10 @@ realizes some 'host of immune response role' - age - A time quality inhering in a bearer by virtue of how long the bearer has existed. + age + A time quality inhering in a bearer by virtue of how long the bearer has existed. - age + age @@ -6796,11 +6796,11 @@ realizes some 'host of immune response role' - biological sex - An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + biological sex + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. CS5 - biological sex + biological sex @@ -6809,10 +6809,10 @@ realizes some 'host of immune response role' - time - A quality in which events occur in sequence. + time + A quality in which events occur in sequence. - time + time @@ -6821,10 +6821,10 @@ realizes some 'host of immune response role' - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + physical quality + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - physical quality + physical quality @@ -6833,10 +6833,10 @@ realizes some 'host of immune response role' - physical object quality - A quality which inheres in a continuant. + physical object quality + A quality which inheres in a continuant. - physical object quality + physical object quality @@ -6845,11 +6845,11 @@ realizes some 'host of immune response role' - organismal quality - A quality that inheres in an entire organism or part of an organism. + organismal quality + A quality that inheres in an entire organism or part of an organism. CS8 - organismal quality + organismal quality @@ -6858,11 +6858,11 @@ realizes some 'host of immune response role' - protein - antithrombin III is a protein - An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. + protein + antithrombin III is a protein + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. - protein + protein @@ -6871,12 +6871,12 @@ realizes some 'host of immune response role' - region - A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. - primary structure of sequence macromolecule - sequence + region + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + primary structure of sequence macromolecule + sequence - region + region @@ -6885,10 +6885,10 @@ realizes some 'host of immune response role' - sequence_assembly - A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + sequence_assembly + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. - sequence_assembly + sequence_assembly @@ -6897,10 +6897,10 @@ realizes some 'host of immune response role' - assembly - A region of the genome of known length that is composed by ordering and aligning two or more different regions. + assembly + A region of the genome of known length that is composed by ordering and aligning two or more different regions. - assembly + assembly @@ -6909,10 +6909,10 @@ realizes some 'host of immune response role' - experimental_feature - A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + experimental_feature + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. - experimental_feature + experimental_feature @@ -6921,10 +6921,10 @@ realizes some 'host of immune response role' - material anatomical entity - Anatomical entity that has mass. + material anatomical entity + Anatomical entity that has mass. - material anatomical entity + material anatomical entity @@ -6933,10 +6933,10 @@ realizes some 'host of immune response role' - anatomical cluster - Anatomical group that has its parts adjacent to one another. + anatomical cluster + Anatomical group that has its parts adjacent to one another. - anatomical cluster + anatomical cluster @@ -6945,11 +6945,11 @@ realizes some 'host of immune response role' - time unit - A unit which is a standard measure of the dimension in which events occur in sequence. + time unit + A unit which is a standard measure of the dimension in which events occur in sequence. CS7 - time unit + time unit @@ -7019,7 +7019,7 @@ realizes some 'host of immune response role' organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release - PERSON:Alan Ruttenberg + PERSON:Alan Ruttenberg organizational term @@ -7192,8 +7192,8 @@ realizes some 'host of immune response role' CS13 - A reference to a place on the Earth, by its name or by its geographical location. - geographic location + A reference to a place on the Earth, by its name or by its geographical location. + geographic location diff --git a/views/obi.obo b/views/obi.obo index a02ad5af..fe71962a 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: obi/2021-08-18/obi.obo -date: 18:08:2021 11:00 +data-version: obi/2022-01-03/obi.obo +date: 03:01:2022 13:09 remark: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. ontology: obi.obo property_value: defaultLanguage "en" xsd:string @@ -67,7 +67,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string -property_value: owl:versionInfo "2021-08-18" xsd:string +property_value: owl:versionInfo "2022-01-03" xsd:string [Term] id: APOLLO_SV:00000008 @@ -207,7 +207,7 @@ is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000024 -name: fiat object +name: fiat object part is_a: BFO:0000040 ! material entity [Term] @@ -314,6 +314,12 @@ id: BFO:0000182 name: history is_a: BFO:0000015 ! process +[Term] +id: CHEBI:145810 +name: insulin +def: "A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies." [] +is_a: CHEBI:16670 ! peptide + [Term] id: CHEBI:15377 name: water @@ -344,6 +350,18 @@ name: ammonia def: "An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:16247 +name: phospholipid +def: "A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:16301 +name: nitrite +def: "The nitrogen oxoanion formed by loss of a proton from nitrous acid." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:16526 name: carbon dioxide @@ -374,6 +392,12 @@ name: mycophenolic acid def: "A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:16919 +name: creatine +def: "A glycine derivative having methyl and amidino groups attached to the nitrogen." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:16990 name: bilirubin IXalpha @@ -386,6 +410,12 @@ name: deoxyribonucleic acid def: "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms." [] is_a: CHEBI:33696 ! nucleic acid +[Term] +id: CHEBI:17026 +name: progesterone +def: "A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:17137 name: hydrogensulfite @@ -403,6 +433,12 @@ name: glucose def: "An aldohexose used as a source of energy and metabolic intermediate." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:17347 +name: testosterone +def: "An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:17423 name: methemoglobin @@ -443,6 +479,12 @@ is_a: CHEBI:23367 ! molecular entity id: CHEBI:20067 name: 3-hydroxybutyric acid def: "A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics." [] +is_a: CHEBI:35366 ! fatty acid + +[Term] +id: CHEBI:22868 +name: bile salt +def: "A sodium salt of the conjugate of any bile acid with either glycine or taurine." [] is_a: CHEBI:23367 ! molecular entity [Term] @@ -456,6 +498,12 @@ id: CHEBI:23528 name: cytochalasin is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:23965 +name: estradiol +def: "A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:23995 name: N-ethyl-N-nitrosourea @@ -574,7 +622,7 @@ is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:31624 -name: fluorescein +name: fluorescein (lactone form) def: "A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy." [] is_a: OBI:0002744 ! molecular label @@ -664,6 +712,12 @@ id: CHEBI:35143 name: hemoglobin is_a: CHEBI:33839 ! macromolecule +[Term] +id: CHEBI:35366 +name: fatty acid +def: "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:35729 name: gadolinium molecular entity @@ -716,6 +770,24 @@ id: CHEBI:37989 name: Cy5 dye is_a: OBI:0002744 ! molecular label +[Term] +id: CHEBI:39025 +name: high-density lipoprotein +def: "A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. They are synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport)." [] +is_a: CHEBI:6495 ! lipoprotein + +[Term] +id: CHEBI:39026 +name: low-density lipoprotein +def: "A class of lipoproteins of small size (18-25 nm) and low density (1.019-1.063 g/ml) particles with a core composed mainly of cholesterol esters and smaller amounts of triglycerides. The surface monolayer consists mostly of phospholipids, a single copy of apolipoprotein B-100, and free cholesterol molecules. The main function of LDL is to transport cholesterol and cholesterol esters from the liver. Excessive levels are associated with cardiovascular disease." [] +is_a: CHEBI:6495 ! lipoprotein + +[Term] +id: CHEBI:39027 +name: very-low-density lipoprotein +def: "A class of lipoproteins of large size (30-80 nm), very low density (0.93-1.006 g/ml) particles with a core composed mainly of triglycerides and a surface monolayer of phospholipids and cholesterol into which are imbedded the apolipoproteins B, E, and C. VLDL facilitate the transport of endogenously made triglycerides to extrahepatic tissues." [] +is_a: CHEBI:6495 ! lipoprotein + [Term] id: CHEBI:39123 name: calcium cation @@ -731,7 +803,7 @@ is_a: CHEBI:23367 ! molecular entity id: CHEBI:39867 name: valproic acid def: "A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem." [] -is_a: CHEBI:23367 ! molecular entity +is_a: CHEBI:35366 ! fatty acid [Term] id: CHEBI:42098 @@ -861,11 +933,27 @@ name: oxygen radical def: "An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:6495 +name: lipoprotein +def: "A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [] +is_a: CHEBI:33839 ! macromolecule + [Term] id: CHEBI:81567 name: thyroid stimulating hormone is_a: CHEBI:33839 ! macromolecule +[Term] +id: CHEBI:81568 +name: Luteinizing hormone +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:81569 +name: Follicle stimulating hormone +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:86319 name: 25-hydroxyvitamin D2 @@ -880,16 +968,17 @@ is_a: CHEBI:23367 ! molecular entity [Term] id: CHMO:0000087 -name: fluorescence microscopy -def: "Any type of microscopy where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores." [] +name: fluorescence microscopy assay +def: "Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores." [] synonym: "fluorescence imaging" EXACT [] synonym: "fluorescence microscopic imaging" EXACT [] synonym: "FM" EXACT [] -is_a: OBI:0002119 ! microscopy assay +is_a: CHMO:0000102 ! light microscopy assay +is_a: OBI:0001501 ! fluorescence detection assay [Term] id: CHMO:0000089 -name: confocal fluorescence microscopy +name: confocal fluorescence microscopy assay def: "Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence." [] synonym: "CLSM" EXACT [] synonym: "confocal fluorescence imaging" EXACT [] @@ -904,7 +993,7 @@ is_a: OBI:0002119 ! microscopy assay [Term] id: CHMO:0000102 -name: light microscopy +name: light microscopy assay def: "Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image." [] synonym: "light microscopy" EXACT [] synonym: "OM" EXACT [] @@ -1020,7 +1109,7 @@ is_a: CL:0000000 ! cell id: CL:0000540 name: neuron def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [] -is_a: CL:0000000 ! cell +is_a: CL:0002319 ! neural cell [Term] id: CL:0000542 @@ -1106,6 +1195,12 @@ def: "Any of the immature or mature forms of a granular leukocyte that in its ma is_a: CL:0000003 ! native cell is_a: CL:0000738 ! leukocyte +[Term] +id: CL:0000776 +name: immature neutrophil +def: "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." [] +is_a: CL:0000775 ! neutrophil + [Term] id: CL:0000786 name: plasma cell @@ -1154,6 +1249,12 @@ name: myelocyte def: "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses." [] is_a: CL:0000003 ! native cell +[Term] +id: CL:0002319 +name: neural cell +def: "A cell that is part of the nervous system." [] +is_a: CL:0000000 ! cell + [Term] id: CL:0011114 name: segmented neutrophil of bone marrow @@ -1172,25 +1273,31 @@ is_a: CLO:0000001 ! cell line cell [Term] id: CLO:0000019 -name: immortal cell line cell +name: 永生细胞系细胞 is_a: CLO:0000001 ! cell line cell [Term] id: CLO:0000031 -name: cell line +name: 细胞系 is_a: OBI:0001905 ! secondary cultured cell population [Term] id: CLO:0009828 name: immortal cell line def: "A cell line that is expected to be capable of indefinite propagation in an vitro culture." [] -is_a: CLO:0000031 ! cell line +is_a: CLO:0000031 ! 细胞系 [Term] id: CLO:0009829 name: mortal cell line def: "A cell line is able to support only a limited number of passages in vitro." [] -is_a: CLO:0000031 ! cell line +is_a: CLO:0000031 ! 细胞系 + +[Term] +id: COB:0000080 +name: complex of molecular entities +def: "A complex of two or more molecular entities that are not covalently bound." [] +is_a: BFO:0000040 ! material entity [Term] id: ENVO:00001998 @@ -3724,6 +3831,18 @@ name: Daphnia synonym: "common water fleas" EXACT [] is_a: NCBITaxon:197562 ! Pancrustacea +[Term] +id: NCBITaxon:7147 +name: Diptera +synonym: "flies" EXACT [] +is_a: NCBITaxon:197562 ! Pancrustacea + +[Term] +id: NCBITaxon:7157 +name: Culicidae +synonym: "mosquitos" EXACT [] +is_a: NCBITaxon:7147 ! Diptera + [Term] id: NCBITaxon:716545 name: saccharomyceta @@ -3733,7 +3852,7 @@ is_a: NCBITaxon:4890 ! Ascomycota id: NCBITaxon:7227 name: Drosophila melanogaster synonym: "fruit fly" EXACT [] -is_a: NCBITaxon:197562 ! Pancrustacea +is_a: NCBITaxon:7147 ! Diptera [Term] id: NCBITaxon:7742 @@ -4405,9 +4524,9 @@ is_a: BFO:0000040 ! material entity [Term] id: OBI:0000182 -name: nuclear magnetic resonance 3D structure determination assay -def: "A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample." [] -is_a: OBI:0600045 ! 3D structure determination assay +name: NMR 3D molecular structure determination assay +def: "A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample." [] +is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0000185 @@ -5714,8 +5833,8 @@ is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000522 name: vial -def: "A vial is a cylindrical container often made from glass tubing." [] -is_a: OBI:0000601 ! chromatography consumable +def: "A container made from solid material and primarily used for holding liquid." [] +is_a: OBI:0000967 ! container [Term] id: OBI:0000523 @@ -7399,7 +7518,7 @@ name: test tube def: "A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material" [] synonym: "collection tube" EXACT [] synonym: "sample tube" EXACT [] -is_a: OBI:0000967 ! container +is_a: OBI:0000522 ! vial [Term] id: OBI:0000837 @@ -7445,9 +7564,11 @@ is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000844 -name: hospital +name: obsolete hospital def: "A medical organization at which sick or injured people are given clinical care" [] -is_a: OBI:0000245 ! organization +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true +replaced_by: OMRSE:00000056 [Term] id: OBI:0000845 @@ -7790,9 +7911,9 @@ is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0000912 -name: X-ray crystallography assay -def: "A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest." [] -is_a: OBI:0600045 ! 3D structure determination assay +name: X-ray crystallography 3D molecular structure determination assay +def: "A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest." [] +is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0000913 @@ -7816,6 +7937,7 @@ is_a: OBI:0302893 ! storage id: OBI:0000916 name: flow cytometry assay def: "A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution." [] +synonym: "FACS" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] @@ -7843,7 +7965,7 @@ is_a: OBI:0600006 ! killing [Term] id: OBI:0000920 name: cytometric bead array assay -def: "An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes." [] +def: "An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest." [] synonym: "Luminex assay" EXACT [] is_a: OBI:0000443 ! analyte assay @@ -8996,7 +9118,7 @@ is_a: OBI:0400169 ! microscope [Term] id: OBI:0001106 name: pulsed-field gel electrophoresis system -def: "A gel electrophoresis system that is used to separate very large molecules of DNA." [] +def: "A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction." [] is_a: OBI:0001121 ! gel electrophoresis system [Term] @@ -9087,8 +9209,7 @@ is_a: OBI:0400143 ! fluorometer [Term] id: OBI:0001121 name: gel electrophoresis system -def: "A device that moves charged particles through a medium by using an electric field induced by electrodes." [] -synonym: "electrophoresis system" EXACT [] +def: "An electrophoresis system in which an electric field is applied to a gel matrix" [] is_a: OBI:0001053 ! electrophoresis system [Term] @@ -9168,7 +9289,7 @@ is_a: OBI:0000932 ! material separation device id: OBI:0001134 name: agarose gel electrophoresis system def: "A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field." [] -is_a: OBI:0001053 ! electrophoresis system +is_a: OBI:0001121 ! gel electrophoresis system [Term] id: OBI:0001135 @@ -9229,14 +9350,14 @@ is_a: OBI:0000924 ! labeled specimen [Term] id: OBI:0001144 name: binding constant -def: "A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process" [] -is_a: OBI:0001181 ! binding datum +def: "A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed." [] +is_a: OBI:0003142 ! quantitative binding datum [Term] id: OBI:0001145 -name: 3D structure determination of bound complex assay -def: "A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration." [] -is_a: OBI:0600045 ! 3D structure determination assay +name: 3D structure determination of bound molecular complex assay +def: "A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration." [] +is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0001146 @@ -9462,8 +9583,8 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0001182 name: negative binding datum -def: "A binding datum that states that there is no significant disposition of two or more entities to form a complex" [] -is_a: OBI:0001181 ! binding datum +def: "A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex." [] +is_a: OBI:0003141 ! categorical binding datum [Term] id: OBI:0001183 @@ -9543,9 +9664,10 @@ is_a: GO:0001816 ! cytokine production [Term] id: OBI:0001194 name: ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells -def: "An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|ELISPOT" EXACT [] -is_a: OBI:0001264 ! biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001195 @@ -9556,9 +9678,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001196 name: cytometric bead array assay measuring epitope specific IP-10 production by T cells -def: "An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|cytometric bead array" EXACT [] -is_a: OBI:0001308 ! biological activity assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001197 @@ -9568,10 +9691,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001198 -name: biological activity assay measuring epitope specific interleukin-27 production by T cells +name: assay measuring epitope specific interleukin-27 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001199 @@ -9600,9 +9723,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001203 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells -def: "An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|RNA/DNA detection" EXACT [] -is_a: OBI:0001264 ! biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001204 @@ -9619,9 +9743,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001206 name: ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells -def: "An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|ELISPOT" EXACT [] -is_a: OBI:0001233 ! biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001207 @@ -9638,17 +9763,18 @@ is_a: GO:0042110 ! T cell activation [Term] id: OBI:0001209 -name: biological activity assay measuring epitope specific interleukin-10 production by T cells +name: assay measuring epitope specific interleukin-10 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001210 name: cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells -def: "An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects transforming growth factor-beta production by T cells" [] synonym: "TGFb release|cytometric bead array" EXACT [] -is_a: OBI:0001264 ! biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001211 @@ -9678,23 +9804,24 @@ is_a: OBI:0001497 ! biological activity assay measuring epitope specific perfori [Term] id: OBI:0001216 name: cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|bioassay" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:0001217 -name: biological activity assay measuring epitope specific interleukin-22 production by T cells +name: assay measuring epitope specific interleukin-22 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001218 -name: biological activity assay measuring epitope specific interleukin-8 production by T cells +name: assay measuring epitope specific interleukin-8 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001219 @@ -9706,9 +9833,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001220 name: cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells -def: "An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|bioassay" EXACT [] -is_a: OBI:0001209 ! biological activity assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:0001221 @@ -9719,16 +9847,18 @@ is_a: OBI:0001248 ! ChIP-chip assay [Term] id: OBI:0001222 name: ELISA measuring epitope specific RANTES production by T cells -def: "An assay of epitope specific RANTES production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|ELISA" EXACT [] -is_a: OBI:0001232 ! biological activity assay measuring epitope specific RANTES production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells [Term] id: OBI:0001223 name: cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells -def: "An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|cytometric bead array" EXACT [] -is_a: OBI:0001449 ! biological activity assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001225 @@ -9745,9 +9875,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001227 name: ELISPOT assay measuring epitope specific interleukin-6 production by T cells -def: "An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-6 production by T cells" [] synonym: "IL-6 release|ELISPOT" EXACT [] -is_a: OBI:0001451 ! biological activity assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001228 @@ -9759,37 +9890,39 @@ is_a: OBI:0001495 ! biological activity assay measuring epitope specific T cell [Term] id: OBI:0001229 name: plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex -def: "A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay." [] +def: "A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor." [] synonym: "dissociation constant KD|surface plasmon resonance (SPR)|nM" EXACT [] +is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0002097 ! assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex [Term] id: OBI:0001230 -name: biological activity assay measuring epitope specific interleukin-5 production by T cells +name: assay measuring epitope specific interleukin-5 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001231 name: ELISA measuring epitope specific transforming growth factor-beta production by T cells -def: "An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|ELISA" EXACT [] -is_a: OBI:0001264 ! biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001232 -name: biological activity assay measuring epitope specific RANTES production by T cells +name: assay measuring epitope specific RANTES production by T cells def: "A T cell epitope specific cytokine production assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001233 -name: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +name: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells def: "A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001234 @@ -9806,23 +9939,25 @@ is_a: OBI:0001463 ! transcription profiling by array assay [Term] id: OBI:0001236 name: ELISA measuring epitope specific interleukin-22 production by T cells -def: "An assay of epitope specific interleukin-22 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|ELISA" EXACT [] -is_a: OBI:0001217 ! biological activity assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells [Term] id: OBI:0001237 -name: biological activity assay measuring epitope specific interleukin-21 production by T cells +name: assay measuring epitope specific interleukin-21 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001238 name: ELISA measuring epitope specific interleukin-9 production by T cells -def: "An assay of epitope specific interleukin-9 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|ELISA" EXACT [] -is_a: OBI:0001253 ! biological activity assay measuring interleukin-9 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells [Term] id: OBI:0001239 @@ -9833,38 +9968,42 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001240 name: intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells -def: "An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|ICS" EXACT [] -is_a: OBI:0001451 ! biological activity assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:0001241 name: cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells -def: "An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|bioassay" EXACT [] -is_a: OBI:0001450 ! biological activity assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:0001242 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells -def: "A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor production by T cells." [] synonym: "TNFa release|RNA/DNA detection" EXACT [] -is_a: OBI:0001416 ! biological activity assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells is_a: OBI:0001788 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001243 name: cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells -def: "An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|cytometric bead array" EXACT [] -is_a: OBI:0001465 ! biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001244 name: ELISA measuring epitope specific interleukin-23 production by T cells -def: "An assay of epitope specific interleukin-23 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|ELISA" EXACT [] -is_a: OBI:0001363 ! biological activity assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells [Term] id: OBI:0001245 @@ -9876,9 +10015,10 @@ is_a: OBI:0001497 ! biological activity assay measuring epitope specific perfori [Term] id: OBI:0001246 name: ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|ELISA" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001247 @@ -9911,10 +10051,10 @@ replaced_by: OBI:0000916 [Term] id: OBI:0001251 -name: biological activity assay measuring epitope specific interleukin-13 production by T cells +name: assay measuring epitope specific interleukin-13 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001252 @@ -9924,10 +10064,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001253 -name: biological activity assay measuring interleukin-9 production by T cells +name: assay measuring interleukin-9 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001254 @@ -9939,9 +10079,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001255 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells -def: "An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001230 ! biological activity assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:0001256 @@ -9972,16 +10113,18 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001260 name: ELISA measuring epitope specific interleukin-3 production by T cells -def: "An assay of epitope specific interleukin-3 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|ELISA" EXACT [] -is_a: OBI:0001406 ! biological activity assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001261 name: ELISA measuring epitope specific interleukin-1 alpha production by T cells -def: "An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|ELISA" EXACT [] -is_a: OBI:0001388 ! biological activity assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells [Term] id: OBI:0001262 @@ -9999,10 +10142,10 @@ is_a: OBI:0001495 ! biological activity assay measuring epitope specific T cell [Term] id: OBI:0001264 -name: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +name: assay measuring epitope specific transforming growth factor-beta production by T cells def: "A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001265 @@ -10026,23 +10169,25 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001268 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells -def: "An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001391 ! biological activity assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells [Term] id: OBI:0001269 name: biological activity assay measuring epitope specific cytotoxic T cell degranulation def: "A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation." [] synonym: "degranulation|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001270 name: cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells -def: "An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|bioassay" EXACT [] -is_a: OBI:0001264 ! biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001271 @@ -10054,16 +10199,18 @@ is_a: OBI:0001177 ! RNA sequencing assay [Term] id: OBI:0001272 name: ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|ELISPOT" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001273 name: cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells -def: "An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|bioassay" EXACT [] -is_a: OBI:0001230 ! biological activity assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:0001274 @@ -10081,17 +10228,18 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001276 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells." [] synonym: "CCL1/TCA-3 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001277 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:0001278 @@ -10102,23 +10250,25 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001279 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells -def: "An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001217 ! biological activity assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells [Term] id: OBI:0001280 -name: biological activity assay measuring epitope specific interleukin-16 production by T cells +name: assay measuring epitope specific interleukin-16 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001281 name: ELISA measuring epitope specific IP-10 production by T cells -def: "An assay of epitope specific IP-10 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|ELISA" EXACT [] -is_a: OBI:0001308 ! biological activity assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells [Term] id: OBI:0001282 @@ -10129,16 +10279,18 @@ is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0001283 name: ELISA measuring epitope specific interleukin-15 production by T cells -def: "An assay of epitope specific interleukin-15 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|ELISA" EXACT [] -is_a: OBI:0001292 ! biological activity assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells [Term] id: OBI:0001284 name: cytometric bead array assay measuring epitope specific interleukin-12 production by T cells -def: "An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|cytometric bead array" EXACT [] -is_a: OBI:0001391 ! biological activity assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001285 @@ -10155,17 +10307,18 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001288 name: ELISA measuring epitope specific lymphotoxin A production by T cells -def: "An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|ELISA" EXACT [] is_a: OBI:0001246 ! ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001327 ! biological activity assay measuring epitope specific lymphotoxin A production by T cells +is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells [Term] id: OBI:0001289 name: cytometric bead array assay measuring epitope specific interleukin-5 production by T cells -def: "An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|cytometric bead array" EXACT [] -is_a: OBI:0001230 ! biological activity assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001290 @@ -10176,16 +10329,17 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001291 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells -def: "An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001292 -name: biological activity assay measuring epitope specific interleukin-15 production by T cells +name: assay measuring epitope specific interleukin-15 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001293 @@ -10201,66 +10355,74 @@ is_a: OBI:0001305 ! genotype information [Term] id: OBI:0001295 -name: biological activity assay measuring epitope specific interleukin-17 production by T cells +name: assay measuring epitope specific interleukin-17 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001296 name: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells -def: "An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|cytometric bead array" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001297 name: cytometric bead array assay measuring epitope specific interleukin-10 production by T cells -def: "An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|cytometric bead array" EXACT [] -is_a: OBI:0001209 ! biological activity assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001298 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells -def: "An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001237 ! biological activity assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells [Term] id: OBI:0001299 name: intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells -def: "An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|ICS" EXACT [] -is_a: OBI:0001230 ! biological activity assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:0001300 name: cytometric bead array assay measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|cytometric bead array" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001301 name: cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells -def: "An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|bioassay" EXACT [] -is_a: OBI:0001280 ! biological activity assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001302 name: ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|ELISA" EXACT [] -is_a: OBI:0001333 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells [Term] id: OBI:0001303 name: intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells -def: "An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|ICS" EXACT [] -is_a: OBI:0001233 ! biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:0001304 @@ -10289,17 +10451,18 @@ is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0001308 -name: biological activity assay measuring epitope specific IP-10 production by T cells +name: assay measuring epitope specific IP-10 production by T cells def: "A T cell epitope specific cytokine production assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001309 name: intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells -def: "An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|ICS" EXACT [] -is_a: OBI:0001251 ! biological activity assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells [Term] id: OBI:0001310 @@ -10310,9 +10473,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001311 name: X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex -def: "A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay." [] +def: "A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex." [] synonym: "3D structure|x-ray crystallography|angstroms" EXACT [] -is_a: OBI:0001999 ! 3D structure determining assay of a T cell epitope:MHC:TCR complex +is_a: OBI:0000912 ! X-ray crystallography 3D molecular structure determination assay +is_a: OBI:0001999 ! 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex [Term] id: OBI:0001313 @@ -10329,9 +10493,10 @@ is_a: GO:0035399 ! helper T cell enhancement of B cell mediated immune response [Term] id: OBI:0001315 name: ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|ELISA" EXACT [] -is_a: OBI:0001276 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells [Term] id: OBI:0001316 @@ -10343,9 +10508,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001317 name: flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex -def: "A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay." [] +def: "A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor." [] synonym: "T cell- APC binding|binding assay" EXACT [] -is_a: OBI:1110124 ! assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:1110124 ! assay measuring qualitative binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:0001318 @@ -10357,9 +10523,10 @@ is_a: OBI:2100023 ! protein assay [Term] id: OBI:0001319 name: cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|bioassay" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:0001322 @@ -10384,23 +10551,25 @@ is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific [Term] id: OBI:0001325 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells -def: "An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|RNA/DNA detection" EXACT [] -is_a: OBI:0001232 ! biological activity assay measuring epitope specific RANTES production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells [Term] id: OBI:0001326 name: cytometric bead array assay measuring epitope specific interleukin-4 production by T cells -def: "An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-4 production by T cells" [] synonym: "IL-4 release|cytometric bead array" EXACT [] -is_a: OBI:0001450 ! biological activity assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001327 -name: biological activity assay measuring epitope specific lymphotoxin A production by T cells +name: assay measuring epitope specific lymphotoxin A production by T cells def: "A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|biological activity" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001328 @@ -10417,9 +10586,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001330 name: ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|ELISA" EXACT [] -is_a: OBI:0001459 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells [Term] id: OBI:0001331 @@ -10435,10 +10605,10 @@ is_a: OBI:0000634 ! DNA methylation profiling assay [Term] id: OBI:0001333 -name: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +name: assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001334 @@ -10468,51 +10638,57 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001339 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells -def: "An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001450 ! biological activity assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:0001341 name: cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells -def: "An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|bioassay" EXACT [] -is_a: OBI:0001233 ! biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:0001342 name: intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells -def: "An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|ICS" EXACT [] -is_a: OBI:0001237 ! biological activity assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells [Term] id: OBI:0001343 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells -def: "An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001465 ! biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells [Term] id: OBI:0001344 name: ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells -def: "An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|ELISA" EXACT [] -is_a: OBI:0001465 ! biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells [Term] id: OBI:0001345 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001346 name: ELISA measuring epitope specific interleukin-21 production by T cells -def: "An assay of epitope specific interleukin-21 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|ELISA" EXACT [] -is_a: OBI:0001237 ! biological activity assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells [Term] id: OBI:0001348 @@ -10524,16 +10700,18 @@ is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific [Term] id: OBI:0001349 name: cytometric bead array assay measuring epitope specific interleukin-13 production by T cells -def: "An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|cytometric bead array" EXACT [] -is_a: OBI:0001251 ! biological activity assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001350 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells." [] synonym: "IFNg release|RNA/DNA detection" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:0001351 @@ -10551,31 +10729,34 @@ is_a: OBI:0001364 ! genetic alteration information [Term] id: OBI:0001353 name: cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells -def: "A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects tumor necrosis factor production by T cells." [] synonym: "TNFa release|cytometric bead array" EXACT [] is_a: OBI:0001368 ! cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! biological activity assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells [Term] id: OBI:0001354 name: ELISPOT assay measuring epitope specific interleukin-17 production by T cells -def: "An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|ELISPOT" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001356 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells -def: "An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells." [] synonym: "IFNb release|RNA/DNA detection" EXACT [] -is_a: OBI:0001390 ! biological activity assay measuring epitope specific interferon-beta production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells [Term] id: OBI:0001357 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells -def: "An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|RNA/DNA detection" EXACT [] -is_a: OBI:0001233 ! biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:0001358 @@ -10586,16 +10767,18 @@ is_a: OBI:0000115 ! intervention design [Term] id: OBI:0001359 name: ELISA measuring epitope specific interleukin-8 production by T cells -def: "An assay of epitope specific interleukin-8 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|ELISA" EXACT [] -is_a: OBI:0001218 ! biological activity assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells [Term] id: OBI:0001360 name: cytometric bead array assay measuring epitope specific interleukin-6 production by T cells -def: "An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|cytometric bead array" EXACT [] -is_a: OBI:0001451 ! biological activity assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001361 @@ -10613,10 +10796,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001363 -name: biological activity assay measuring epitope specific interleukin-23 production by T cells +name: assay measuring epitope specific interleukin-23 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001364 @@ -10640,16 +10823,18 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001367 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells -def: "An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001209 ! biological activity assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:0001368 name: cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|cytometric bead array" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001369 @@ -10660,9 +10845,10 @@ is_a: OBI:0001352 ! allele information [Term] id: OBI:0001370 name: intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|ICS" EXACT [] -is_a: OBI:0001345 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells [Term] id: OBI:0001371 @@ -10686,9 +10872,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001376 name: intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells -def: "An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|ICS" EXACT [] -is_a: OBI:0001406 ! biological activity assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001377 @@ -10699,23 +10886,25 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001378 name: ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|ELISA" EXACT [] -is_a: OBI:0001345 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells [Term] id: OBI:0001379 name: cytometric bead array assay measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|cytometric bead array" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001380 -name: biological activity assay measuring epitope specific interleukin-18 production by T cells +name: assay measuring epitope specific interleukin-18 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001381 @@ -10727,30 +10916,34 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001382 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells -def: "An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001198 ! biological activity assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells [Term] id: OBI:0001383 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells -def: "An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001308 ! biological activity assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells [Term] id: OBI:0001384 name: cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells -def: "An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|bioassay" EXACT [] -is_a: OBI:0001406 ! biological activity assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001385 name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|ICS" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001386 @@ -10767,31 +10960,32 @@ is_a: OBI:0001444 ! genotyping design [Term] id: OBI:0001388 -name: biological activity assay measuring epitope specific interleukin-1 alpha production by T cells +name: assay measuring epitope specific interleukin-1 alpha production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001389 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells -def: "An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001451 ! biological activity assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:0001390 -name: biological activity assay measuring epitope specific interferon-beta production by T cells +name: assay measuring epitope specific interferon-beta production by T cells def: "A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001391 -name: biological activity assay measuring epitope specific interleukin-12 production by T cells +name: assay measuring epitope specific interleukin-12 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001392 @@ -10817,9 +11011,10 @@ is_a: GO:0043316 ! cytotoxic T cell degranulation [Term] id: OBI:0001395 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells -def: "An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001363 ! biological activity assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells [Term] id: OBI:0001396 @@ -10830,9 +11025,10 @@ is_a: OBI:0000115 ! intervention design [Term] id: OBI:0001397 name: cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells -def: "An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|cytometric bead array" EXACT [] -is_a: OBI:0001600 ! biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001398 @@ -10849,10 +11045,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001400 -name: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +name: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001401 @@ -10863,9 +11059,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001402 name: promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay." [] +def: "A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|reporter gene assay" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0000913 ! promoter activity detection by reporter gene assay +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:0001403 @@ -10883,23 +11080,24 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0001405 name: cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|cytometric bead array" EXACT [] -is_a: OBI:0001333 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001406 -name: biological activity assay measuring epitope specific interleukin-3 production by T cells +name: assay measuring epitope specific interleukin-3 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001407 name: biological activity assay measuring epitope specific T cell activation def: "A T cell epitope dependent biological activity assay that detects T cell activation." [] synonym: "activation|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001408 @@ -10928,23 +11126,25 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001412 name: cytometric bead array assay measuring epitope specific RANTES production by T cells -def: "An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|cytometric bead array" EXACT [] -is_a: OBI:0001232 ! biological activity assay measuring epitope specific RANTES production by T cells +is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001413 name: cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells -def: "An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|bioassay" EXACT [] -is_a: OBI:0001451 ! biological activity assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:0001414 -name: biological activity assay measuring epitope specific interferon-gamma production by T cells +name: assay measuring epitope specific interferon-gamma production by T cells def: "A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001415 @@ -10955,10 +11155,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001416 -name: biological activity assay measuring epitope specific tumor necrosis factor production by T cells +name: assay measuring epitope specific tumor necrosis factor production by T cells def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production." [] synonym: "TNFa release|biological activity" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001417 @@ -11043,9 +11243,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001433 name: radio immuno assay measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay." [] +def: "A radio immuno assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|radio immuno assay (RIA)" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0000910 ! radio immuno assay +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:0001435 @@ -11063,16 +11264,18 @@ is_a: OBI:0001269 ! biological activity assay measuring epitope specific cytotox [Term] id: OBI:0001437 name: intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|ICS" EXACT [] -is_a: OBI:0001459 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells [Term] id: OBI:0001438 name: ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|ELISA" EXACT [] -is_a: OBI:0001456 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells [Term] id: OBI:0001439 @@ -11108,10 +11311,10 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001445 -name: biological activity assay measuring epitope specific interleukin-2 production by T cells +name: assay measuring epitope specific interleukin-2 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001446 @@ -11135,38 +11338,39 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001449 -name: biological activity assay measuring epitope specific interleukin-1 beta production by T cells +name: assay measuring epitope specific interleukin-1 beta production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001450 -name: biological activity assay measuring epitope specific interleukin-4 production by T cells +name: assay measuring epitope specific interleukin-4 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001451 -name: biological activity assay measuring epitope specific interleukin-6 production by T cells +name: assay measuring epitope specific interleukin-6 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001452 name: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells -def: "A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay." [] +def: "A reporter cell line analyte detection bioassay that detects tumor necrosis factor production by T cells." [] synonym: "TNFa release|bioassay" EXACT [] -is_a: OBI:0001416 ! biological activity assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells [Term] id: OBI:0001453 name: intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells -def: "An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|ICS" EXACT [] -is_a: OBI:0001327 ! biological activity assay measuring epitope specific lymphotoxin A production by T cells +is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] @@ -11178,30 +11382,32 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001455 name: ELISPOT assay measuring epitope specific interleukin-5 production by T cells -def: "An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|ELISPOT" EXACT [] -is_a: OBI:0001230 ! biological activity assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001456 -name: biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +name: assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001457 name: cytometric bead array assay measuring epitope specific interleukin-8 production by T cells -def: "An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|cytometric bead array" EXACT [] -is_a: OBI:0001218 ! biological activity assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001459 -name: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +name: assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001460 @@ -11238,17 +11444,18 @@ is_a: OBI:0500000 ! study design [Term] id: OBI:0001465 -name: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +name: assay measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001466 name: intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells -def: "An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|ICS" EXACT [] -is_a: OBI:0001391 ! biological activity assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells [Term] id: OBI:0001467 @@ -11350,9 +11557,10 @@ is_a: OBI:0001477 ! lowess transformation [Term] id: OBI:0001482 name: intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells -def: "An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|ICS" EXACT [] -is_a: OBI:0001264 ! biological activity assay measuring epitope specific transforming growth factor-beta production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001483 @@ -11365,7 +11573,7 @@ id: OBI:0001484 name: biological activity assay measuring T cell epitope specific in vivo activity def: "A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment." [] synonym: "in vivo activity|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001485 @@ -11403,9 +11611,10 @@ is_a: OBI:0001478 ! mass spectrometry assay measuring MHC ligand processing and [Term] id: OBI:0001490 name: cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells -def: "An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|cytometric bead array" EXACT [] -is_a: OBI:0001233 ! biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001491 @@ -11425,7 +11634,7 @@ id: OBI:0001493 name: cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition def: "A cell bound MHC binding assay that uses a T cell epitope recognition assay." [] synonym: "qualitative binding|cellular MHC/T cell inhibition" EXACT [] -is_a: OBI:0001550 ! cell bound MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001494 @@ -11438,14 +11647,15 @@ id: OBI:0001495 name: biological activity assay measuring epitope specific T cell helper activity def: "A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function." [] synonym: "helper response|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001496 name: intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells -def: "An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|ICS" EXACT [] -is_a: OBI:0001217 ! biological activity assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells [Term] id: OBI:0001497 @@ -11546,17 +11756,18 @@ is_a: BFO:0000016 ! disposition [Term] id: OBI:0001512 name: cytometric bead array assay measuring epitope specific interleukin-17A production by T cells -def: "A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|cytometric bead array" EXACT [] is_a: OBI:0001296 ! cytometric bead array assay measuring epitope specific interleukin-17 production by T cells -is_a: OBI:0001773 ! biological activity assay measuring epitope specific interleukin-17A production by T cells +is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells [Term] id: OBI:0001513 -name: purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection -def: "A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex +def: "A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|purified MHC/competitive/radioactivity" EXACT [] -is_a: OBI:0001555 ! purified MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001514 @@ -11573,16 +11784,18 @@ is_a: OBI:0001528 ! material service [Term] id: OBI:0001516 -name: cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection -def: "A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding." [] +name: radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex +def: "A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] id: OBI:0001517 -name: cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection -def: "A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex +def: "A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] @@ -11594,24 +11807,27 @@ is_a: OBI:0001351 ! epitope specific tumor necrosis factor superfamily cytokine [Term] id: OBI:0001519 -name: cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection -def: "A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding." [] +name: fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex +def: "A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC/direct/fluorescence" EXACT [] -is_a: OBI:0001579 ! cell lysate MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001579 ! assay measuring binding of a cell-lysate-MHC:ligand complex [Term] id: OBI:0001520 -name: cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001521 name: ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells -def: "An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|ELISA" EXACT [] -is_a: OBI:0001600 ! biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells [Term] id: OBI:0001522 @@ -11623,16 +11839,17 @@ is_a: IAO:0000064 ! algorithm [Term] id: OBI:0001523 name: cytometric bead array assay measuring epitope specific interleukin-17F production by T cells -def: "A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|cytometric bead array" EXACT [] is_a: OBI:0001296 ! cytometric bead array assay measuring epitope specific interleukin-17 production by T cells -is_a: OBI:0001772 ! biological activity assay measuring epitope specific interleukin-17F production by T cells +is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells [Term] id: OBI:0001524 -name: cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding." [] +name: fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "association constant KA|cellular MHC/direct/fluorescence|1/M" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001987 ! assay measuring the association constant [KA] of a MHC:ligand complex [Term] @@ -11675,17 +11892,19 @@ is_a: OBI:0001173 ! service [Term] id: OBI:0001531 -name: purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection -def: "A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand." [] synonym: "half life|purified MHC/direct/fluorescence|min" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001532 name: cytometric bead array assay measuring epitope specific interleukin-9 production by T cells -def: "An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|cytometric bead array" EXACT [] -is_a: OBI:0001253 ! biological activity assay measuring interleukin-9 production by T cells +is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001533 @@ -11695,10 +11914,11 @@ is_a: OBI:0001530 ! data service [Term] id: OBI:0001534 -name: purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection -def: "A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|purified MHC/competitive/fluorescence" EXACT [] -is_a: OBI:0001555 ! purified MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001535 @@ -11715,9 +11935,10 @@ is_a: OBI:0001144 ! binding constant [Term] id: OBI:0001537 -name: purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection -def: "A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|purified MHC/competitive/fluorescence|nM" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -11728,9 +11949,10 @@ is_a: OBI:0001173 ! service [Term] id: OBI:0001539 -name: cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|cellular MHC/competitive/fluorescence|nM" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -11744,38 +11966,43 @@ replaced_by: OBI:0001469 [Term] id: OBI:0001541 -name: purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection -def: "A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex." [] synonym: "on rate|purified MHC/direct/fluorescence|nM^-1s^-1" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001994 ! assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex [Term] id: OBI:0001542 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells -def: "An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001251 ! biological activity assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells [Term] id: OBI:0001543 -name: purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection -def: "A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. " [] +name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 +def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value." [] synonym: "dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM" EXACT [] +is_a: OBI:0001592 ! fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001544 -name: cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection -def: "A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex +def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|lysate MHC/competitive/radioactivity|nM" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001545 name: intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|ICS" EXACT [] -is_a: OBI:0001333 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells [Term] id: OBI:0001546 @@ -11798,17 +12025,18 @@ is_a: OBI:0001144 ! binding constant [Term] id: OBI:0001549 -name: cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection -def: "A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex +def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|cellular MHC/competitive/radioactivity|nM" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001550 -name: cell bound MHC binding assay measuring binding of a MHC:ligand complex -def: "A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells." [] +name: assay measuring binding of a cell-bound-MHC:ligand complex +def: "A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC" EXACT [] -is_a: OBI:0002072 ! assay measuring qualitiative binding of a MHC:ligand complex +is_a: OBI:0002072 ! assay measuring qualitative binding of a MHC:ligand complex [Term] id: OBI:0001551 @@ -11819,17 +12047,17 @@ is_a: OBI:0001173 ! service [Term] id: OBI:0001552 name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells -def: "A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells." [] synonym: "TNFSF11/RANKL release|ICS" EXACT [] is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001607 ! biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells +is_a: OBI:0001607 ! assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells [Term] id: OBI:0001553 name: assay measuring a binding constant of a MHC:ligand complex def: "A MHC:ligand binding assay that measures a binding constant." [] synonym: "binding constant|binding assay" EXACT [] -is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex +is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001554 @@ -11839,17 +12067,18 @@ is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001555 -name: purified MHC binding assay measuring binding of a MHC:ligand complex -def: "A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation." [] +name: assay measuring binding of a purified-MHC:ligand complex +def: "A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC" EXACT [] -is_a: OBI:0002072 ! assay measuring qualitiative binding of a MHC:ligand complex +is_a: OBI:0002072 ! assay measuring qualitative binding of a MHC:ligand complex [Term] id: OBI:0001556 -name: cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection -def: "A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding." [] +name: radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex +def: "A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC/direct/radioactivity" EXACT [] -is_a: OBI:0001579 ! cell lysate MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001579 ! assay measuring binding of a cell-lysate-MHC:ligand complex [Term] id: OBI:0001557 @@ -11859,16 +12088,18 @@ is_a: OBI:0001515 ! material maintenance service [Term] id: OBI:0001558 -name: cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection -def: "A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding." [] +name: radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex +def: "A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half life|cellular MHC/direct/radioactivity|min" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001559 -name: cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half life|cellular MHC/direct/fluorescence|min" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] @@ -11880,17 +12111,18 @@ is_obsolete: true [Term] id: OBI:0001561 -name: cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] id: OBI:0001562 name: intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells -def: "A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|ICS" EXACT [] -is_a: OBI:0001772 ! biological activity assay measuring epitope specific interleukin-17F production by T cells +is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells is_a: OBI:1110178 ! intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells [Term] @@ -11901,59 +12133,64 @@ is_a: OBI:0001528 ! material service [Term] id: OBI:0001564 -name: purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection -def: "A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. " [] +name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 +def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value." [] synonym: "dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM" EXACT [] -is_a: OBI:0001989 ! purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection +is_a: OBI:0001568 ! radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex +is_a: OBI:0001989 ! radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex [Term] id: OBI:0001565 -name: cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection -def: "A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding." [] +name: radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex +def: "A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "half life|lysate MHC/direct/radioactivity|min" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001566 name: 50% dissociation of binding temperature (Tm) -def: "A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. \n" [] +def: "A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound." [] synonym: "melting temperature (Tm)" EXACT [] -is_a: OBI:0001181 ! binding datum +is_a: OBI:0003142 ! quantitative binding datum [Term] id: OBI:0001567 -name: cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection -def: "A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding." [] +name: radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex +def: "A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "off rate|lysate MHC/direct/radioactivity|1/s" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] id: OBI:0001568 -name: purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection -def: "A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex +def: "A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001569 -name: purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection -def: "A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand." [] synonym: "off rate|purified MHC/direct/fluorescence|1/s" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] id: OBI:0001570 -name: biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells +name: assay measuring epitope specific vascular endothelial growth factor production by T cells def: "A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001571 name: equilibrium dissociation constant (KD) approximated by IC50 def: "A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. " [] -is_a: OBI:0001144 ! binding constant -is_a: OBI:0001191 ! half maximal inhibitory concentration (IC50) +is_a: OBI:0001536 ! equilibrium dissociation constant (KD) +is_a: OBI:0003144 ! IC50 binding datum [Term] id: OBI:0001572 @@ -11993,23 +12230,25 @@ is_obsolete: true [Term] id: OBI:0001577 name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells -def: "An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|cytometric bead array" EXACT [] -is_a: OBI:0001217 ! biological activity assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001578 name: ELISA measuring epitope specific vascular endothelial growth factor production by T cells -def: "An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|ELISA" EXACT [] -is_a: OBI:0001570 ! biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells [Term] id: OBI:0001579 -name: cell lysate MHC binding assay measuring binding of a MHC:ligand complex -def: "A MHC binding qualitative binding to ligand assay using MHC in a cell lysate." [] +name: assay measuring binding of a cell-lysate-MHC:ligand complex +def: "A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC" EXACT [] -is_a: OBI:0002072 ! assay measuring qualitiative binding of a MHC:ligand complex +is_a: OBI:0002072 ! assay measuring qualitative binding of a MHC:ligand complex [Term] id: OBI:0001580 @@ -12021,8 +12260,8 @@ is_a: OBI:0001528 ! material service id: OBI:0001581 name: equilibrium dissociation constant (KD) approximated by EC50 def: "A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. " [] -is_a: OBI:0001144 ! binding constant -is_a: OBI:0001180 ! half maximal effective concentration (EC50) +is_a: OBI:0001536 ! equilibrium dissociation constant (KD) +is_a: OBI:0003143 ! EC50 binding datum [Term] id: OBI:0001582 @@ -12041,31 +12280,34 @@ is_a: OBI:0001171 ! half life datum (t 1/2) [Term] id: OBI:0001584 -name: purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display -def: "A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding." [] +name: phage display binding assay measuring binding of a purified-MHC:ligand complex +def: "A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/phage display" EXACT [] -is_a: OBI:0001555 ! purified MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001476 ! phage display binding assay +is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001585 name: cytometric bead array assay measuring epitope specific interleukin-7 production by T cells -def: "An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|cytometric bead array" EXACT [] -is_a: OBI:0001587 ! biological activity assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001586 -name: purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection -def: "A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding." [] +name: radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex +def: "A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand." [] synonym: "half life|purified MHC/direct/radioactivity|min" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001587 -name: biological activity assay measuring epitope specific interleukin-7 production by T cells +name: assay measuring epitope specific interleukin-7 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001588 @@ -12076,17 +12318,18 @@ is_a: GO:0008150 ! biological_process [Term] id: OBI:0001589 name: intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells -def: "A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|ICS" EXACT [] -is_a: OBI:0001773 ! biological activity assay measuring epitope specific interleukin-17A production by T cells +is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells is_a: OBI:1110178 ! intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001590 -name: purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection -def: "A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/fluorescence" EXACT [] -is_a: OBI:0001555 ! purified MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001591 @@ -12096,9 +12339,10 @@ is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001592 -name: purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection -def: "A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] @@ -12109,17 +12353,19 @@ is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001594 -name: cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation" [] +name: fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|cellular MHC/competitive/fluorescence" EXACT [] -is_a: OBI:0001550 ! cell bound MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001595 name: X-ray crystallography assay determining the 3D structure of a MHC:ligand complex -def: "A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay." [] +def: "A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex." [] synonym: "3D structure|x-ray crystallography|angstroms" EXACT [] -is_a: OBI:0002050 ! 3D structure determining assay of a MHC:ligand complex +is_a: OBI:0000912 ! X-ray crystallography 3D molecular structure determination assay +is_a: OBI:0002050 ! 3D molecular structure determination assay of a MHC:ligand complex [Term] id: OBI:0001596 @@ -12142,31 +12388,34 @@ is_a: OBI:0001530 ! data service [Term] id: OBI:0001599 -name: cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection -def: "A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex +def: "A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|cellular MHC/competitive/radioactivity" EXACT [] -is_a: OBI:0001550 ! cell bound MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001600 -name: biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells +name: assay measuring epitope specific granulocyte colony stimulating factor production by T cells def: "A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001601 name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells -def: "An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|cytometric bead array" EXACT [] -is_a: OBI:0001237 ! biological activity assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001602 -name: cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection -def: "A cell bound MHC binding assay that uses radioactivity detection to detect direct binding." [] +name: radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex +def: "A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC/direct/radioactivity" EXACT [] -is_a: OBI:0001550 ! cell bound MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001603 @@ -12177,10 +12426,11 @@ is_a: OBI:0001554 ! rate measurement datum [Term] id: OBI:0001604 -name: purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection -def: "A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding." [] +name: fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex +def: "A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand." [] synonym: "50% dissociation temperature|purified MHC/direct/fluorescence|°C" EXACT [] -is_a: OBI:0001555 ! purified MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001605 @@ -12191,38 +12441,42 @@ is_a: OBI:0001554 ! rate measurement datum [Term] id: OBI:0001606 -name: cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC binding assay that uses fluorescence detection to detect direct binding." [] +name: fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC/direct/fluorescence" EXACT [] -is_a: OBI:0001550 ! cell bound MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001607 -name: biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells +name: assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells def: "An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production." [] synonym: "TNFSF11/RANKL release|biological activity" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001608 -name: purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection -def: "A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding." [] +name: radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex +def: "A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/radioactivity" EXACT [] -is_a: OBI:0001555 ! purified MHC binding assay measuring binding of a MHC:ligand complex +is_a: OBI:0000201 ! radioactivity detection +is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001609 name: intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells -def: "An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|ICS" EXACT [] -is_a: OBI:0001218 ! biological activity assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells [Term] id: OBI:0001610 -name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells -def: "An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay." [] +name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells +def: "A cytometric bead array assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|cytometric bead array" EXACT [] -is_a: OBI:0001363 ! biological activity assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001611 @@ -12241,9 +12495,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001613 -name: purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection -def: "A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex +def: "A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] @@ -12425,7 +12680,7 @@ id: OBI:0001640 name: biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation def: "A B cell epitope dependent biological activity determination assay that detects antigen activation." [] synonym: "antigen activation|biological activity" EXACT [] -is_a: OBI:0001706 ! assay measuring B cell epitope specific biological activity +is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001641 @@ -12446,7 +12701,7 @@ id: OBI:0001643 name: biological activity assay measuring epitope specific immunoglobulin-mediated neutralization def: "A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen." [] synonym: "neutralization |biological activity" EXACT [] -is_a: OBI:0001706 ! assay measuring B cell epitope specific biological activity +is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001644 @@ -12458,107 +12713,122 @@ is_a: OBI:0001704 ! biological activity assay measuring epitope specific activat [Term] id: OBI:0001645 name: calorimetry assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a calorimetric binding assay." [] +def: "A calorimetric binding assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|calorimetry" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001634 ! calorimetric binding assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001646 name: electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex -def: "A B cell epitope 3D structure determination assay that uses an electron microscopy imaging assay." [] +def: "An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex" [] synonym: "3D structure|electron microscopy" EXACT [] -is_a: OBI:0001721 ! 3D structure determining assay of a 3D B cell epitope:antibody complex +is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex +is_a: OBI:0003118 ! electron-microscopy 3D molecular structure determination assay [Term] id: OBI:0001647 name: NMR assay determining the 3D structure of a B cell epitope:antibody complex -def: "A B cell epitope 3D structure determination assay that uses a nuclear magnetic resonance assay." [] +def: "A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex." [] synonym: "3D structure|nuclear magnetic resonance (NMR)" EXACT [] -is_a: OBI:0001721 ! 3D structure determining assay of a 3D B cell epitope:antibody complex +is_a: OBI:0000182 ! NMR 3D molecular structure determination assay +is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex [Term] id: OBI:0001648 name: cross blocking assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an antibody cross-blocking assay." [] +def: "A cross-blocking assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|cross blocking" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001699 ! antibody cross-blocking assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001649 name: RIA measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a radio immuno assay." [] +def: "A radio immuno assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|radio immuno assay (RIA)" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0000910 ! radio immuno assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001650 name: immunoblot assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an immunoblot assay." [] +def: "An immunoblot assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|western blot" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex +is_a: OBI:0001978 ! immunoblot assay [Term] id: OBI:0001651 name: plasmon resonance assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a surface plasmon resonance assay." [] +def: "A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|surface plasmon resonance (SPR)" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0000923 ! surface plasmon resonance binding assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001652 name: immuno staining assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an immuno staining assay." [] +def: "An immuno staining assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|immuno staining" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001632 ! immuno staining assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001653 name: immunoprecipitation assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an immunoprecipitation assay." [] +def: "An immunoprecipitation assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|immunoprecipitation" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001700 ! immunoprecipitation assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001654 name: mass spectrometry assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a mass spectrometry assay." [] +def: "A mass spectrometry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|mass spectrometry" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0000470 ! mass spectrometry assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001655 name: phage display assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a phage display binding assay." [] +def: "A phage display binding assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|phage display" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001476 ! phage display binding assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001656 name: electron microscopy assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an electron microscopy imaging assay." [] +def: "An electron microscopy imaging assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|electron microscopy" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001631 ! electron microscopy imaging assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001657 name: ELISA measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunosorbent assay." [] +def: "An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|ELISA" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001658 name: ELISPOT assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an enzyme-linked immunospot assay." [] +def: "An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|ELISPOT" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001659 name: flow cytometry assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a flow cytometry assay." [] +def: "A flow cytometry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|flow cytometry" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001660 @@ -12570,16 +12840,17 @@ is_a: OBI:0001809 ! biological activity assay measuring epitope specific granzym [Term] id: OBI:0001661 name: chromatography assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an analytical chromatography assay." [] +def: "An analytical chromatography assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|chromatography" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001630 ! analytical chromatography +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001662 name: NMR assay measuring binding of a B cell epitope:antibody complex def: "A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay." [] synonym: "qualitative binding|nuclear magnetic resonance (NMR)" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001663 @@ -12597,24 +12868,27 @@ is_a: OBI:0001810 ! biological activity assay measuring epitope specific granuly [Term] id: OBI:0001665 -name: cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "off rate|cellular MHC/direct/fluorescence|1/s" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] id: OBI:0001666 -name: cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection -def: "A cell bound MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding." [] +name: fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex +def: "A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "on rate|cellular MHC/direct/fluorescence|nM^-1s^-1" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001994 ! assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex [Term] id: OBI:0001667 -name: purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection -def: "A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. " [] +name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 +def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value." [] synonym: "dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM" EXACT [] -is_a: OBI:0001537 ! purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection +is_a: OBI:0001537 ! fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex +is_a: OBI:0001613 ! fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex [Term] id: OBI:0001668 @@ -12672,17 +12946,18 @@ is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001675 name: ELISA measuring epitope specific interleukin-17A production by T cells -def: "A T cell epitope specific interleukin-17A production assay that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|ELISA" EXACT [] -is_a: OBI:0001773 ! biological activity assay measuring epitope specific interleukin-17A production by T cells +is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells is_a: OBI:1110162 ! ELISA measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001676 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells -def: "An assay of epitope specific interleukin-7 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001587 ! biological activity assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells [Term] id: OBI:0001677 @@ -12728,7 +13003,6 @@ is_a: OBI:0001681 ! yeast one-hybrid assay id: OBI:0001683 name: chromosome organization assay by fluorescence in-situ hybridization def: "An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity" [] -synonym: "FISH" EXACT [] is_a: OBI:0001686 ! in-situ hybridization assay [Term] @@ -12825,7 +13099,7 @@ id: OBI:0001698 name: biological activity assay measuring B cell epitope specific in vivo activity def: "A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment." [] synonym: "in vivo activity|biological activity" EXACT [] -is_a: OBI:0001706 ! assay measuring B cell epitope specific biological activity +is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001699 @@ -12845,7 +13119,7 @@ id: OBI:0001701 name: antigen inhibition assay measuring binding of a B cell epitope:antibody complex def: "A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand." [] synonym: "qualitative binding|inhibition by antigen" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001702 @@ -12856,8 +13130,8 @@ is_a: OBI:1110014 ! epitope binding by adaptive immune receptor [Term] id: OBI:0001703 -name: assay measuring qualitiative binding of a B cell epitope:antibody complex -def: "A B cell epitope recognition assay that detects qualitative binding." [] +name: assay measuring qualitative binding of a B cell epitope:antibody complex +def: "An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output." [] synonym: "qualitative binding|binding assay" EXACT [] is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex @@ -12866,21 +13140,21 @@ id: OBI:0001704 name: biological activity assay measuring epitope specific activation of additional immune response in vitro def: "A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity." [] synonym: "secondary in vitro activity|biological activity" EXACT [] -is_a: OBI:0001706 ! assay measuring B cell epitope specific biological activity +is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001705 name: biological activity assay measuring epitope specific antigen inhibition of antibody activity def: "A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen." [] synonym: "antibody activity inhibition|biological activity" EXACT [] -is_a: OBI:0001706 ! assay measuring B cell epitope specific biological activity +is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001706 -name: assay measuring B cell epitope specific biological activity -def: "A B cell epitope recognition assay that detects biological activity." [] +name: assay measuring biological activity resulting from B cell epitope:antibody binding +def: "A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope." [] synonym: "biological activity|any method" EXACT [] -is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex +is_a: OBI:0003127 ! B cell epitope assay [Term] id: OBI:0001707 @@ -12900,7 +13174,7 @@ id: OBI:0001709 name: assay measuring a binding constant of a B cell epitope:antibody complex def: "A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. " [] synonym: "binding constant|binding assay" EXACT [] -is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex +is_a: OBI:0003146 ! assay measuring quantitative binding of an antigen:antibody complex [Term] id: OBI:0001710 @@ -12979,11 +13253,11 @@ is_a: OBI:0001702 ! immunoglobulin binding to epitope [Term] id: OBI:0001721 -name: 3D structure determining assay of a 3D B cell epitope:antibody complex -def: "A B cell epitope recognition assay that characterizes the 3D structure of an antibody / BCR with a ligand." [] +name: 3D molecular structure determination assay of an antigen:antibody complex +def: "A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex." [] synonym: "3D structure|any method" EXACT [] -is_a: OBI:0600045 ! 3D structure determination assay -is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex +is_a: OBI:0001145 ! 3D structure determination of bound molecular complex assay +is_a: OBI:0003127 ! B cell epitope assay [Term] id: OBI:0001722 @@ -13000,10 +13274,11 @@ is_a: OBI:0001709 ! assay measuring a binding constant of a B cell epitope:antib [Term] id: OBI:0001724 -name: biological activity assay measuring epitope specific hemagglutination inhibition -def: "A B cell epitope qualitative binding to antibody assay that uses a viral hemagglutination inhibition assay." [] -synonym: "hemagglutination inhibition|biological activity" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +name: viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex +def: "A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody." [] +synonym: "qualitative binding| hemagglutination inhibition" EXACT [] +is_a: OBI:0000875 ! viral hemagglutination inhibition assay +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001725 @@ -13014,78 +13289,89 @@ is_a: GO:0097280 ! histamine secretion mediated by immunoglobulin [Term] id: OBI:0001726 name: quenching assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an antibody binding detection by fluorescence quenching." [] +def: "A fluorescence quenching assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|quenching" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001727 name: RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a radio immuno assay." [] +def: "A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|radio immuno assay (RIA)|nM" EXACT [] +is_a: OBI:0000910 ! radio immuno assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001728 name: ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an enzyme-linked immunosorbent assay." [] +def: "An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|ELISA|nM" EXACT [] +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001729 name: quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an antibody binding detection by fluorescence quenching assay." [] +def: "A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|quenching|nM" EXACT [] +is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001730 name: surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium association constant (KA) determination assay that uses a surface plasmon resonance assay." [] +def: "A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|surface plasmon resonance (SPR)|1/nM" EXACT [] +is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001731 name: surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay." [] +def: "A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|surface plasmon resonance (SPR)|nM" EXACT [] +is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001732 name: quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium association constant (KA) determination assay that uses an antibody binding detection by fluorescence quenching assay." [] +def: "A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|quenching|1/nM" EXACT [] +is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001733 name: calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium association constant (KA) determination assay that uses a calorimetric binding assay." [] +def: "A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|calorimetry|1/nM" EXACT [] +is_a: OBI:0001634 ! calorimetric binding assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001734 name: calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a calorimetric binding assay." [] +def: "A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|calorimetry|nM" EXACT [] +is_a: OBI:0001634 ! calorimetric binding assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001735 name: ELISA measuring the association constant [KA] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium association constant (KA) determination assay that uses an enzyme-linked immunosorbent assay." [] +def: "An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|ELISA|1/nM" EXACT [] +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001736 name: RIA measuring the association constant [KA] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium association constant (KA) determination assay that uses a radio immuno assay." [] +def: "A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|radio immuno assay (RIA)|1/nM" EXACT [] +is_a: OBI:0000910 ! radio immuno assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] @@ -13100,121 +13386,138 @@ replaced_by: OBI:0001738 [Term] id: OBI:0001738 name: X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex -def: "A B cell epitope 3D structure determination assay that uses an X-ray crystallography assay." [] +def: "A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex." [] synonym: "3D structure|x-ray crystallography|angstroms" EXACT [] -is_a: OBI:0001721 ! 3D structure determining assay of a 3D B cell epitope:antibody complex +is_a: OBI:0000912 ! X-ray crystallography 3D molecular structure determination assay +is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex [Term] id: OBI:0001739 name: surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex -def: "A B cell epitope binding off rate measurement (koff) determination assay that uses a surface plasmon resonance assay." [] +def: "A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody." [] synonym: "off rate|surface plasmon resonance (SPR)|1/s" EXACT [] +is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex [Term] id: OBI:0001740 name: quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex -def: "A B cell epitope binding off rate measurement (koff) determination assay that uses an antibody binding detection by fluorescence quenching assay." [] +def: "A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody." [] synonym: "off rate|quenching|1/s" EXACT [] +is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex [Term] id: OBI:0001741 name: surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex -def: "A B cell epitope on rate measurement (kon) determination assay that uses a surface plasmon resonance assay." [] +def: "A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody." [] synonym: "on rate|surface plasmon resonance (SPR)|M^-1s^-1" EXACT [] +is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex [Term] id: OBI:0001742 name: quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex -def: "A B cell epitope on rate measurement (kon) determination assay that uses an antibody binding detection by fluorescence quenching assay." [] +def: "A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody." [] synonym: "on rate|quenching|M^-1s^-1" EXACT [] +is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex [Term] id: OBI:0001743 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells -def: "An assay of epitope specific interleukin-1 beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|RNA/DNA detection" EXACT [] -is_a: OBI:0001449 ! biological activity assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells [Term] id: OBI:0001744 name: intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells -def: "An assay of epitope specific interleukin-1 alpha production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|ICS" EXACT [] -is_a: OBI:0001388 ! biological activity assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells [Term] id: OBI:0001745 name: ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells -def: "An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|ELISPOT" EXACT [] -is_a: OBI:0001388 ! biological activity assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001746 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells -def: "An assay of epitope specific interleukin-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|RNA/DNA detection" EXACT [] -is_a: OBI:0001388 ! biological activity assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells [Term] id: OBI:0001747 name: cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells -def: "An assay of epitope specific interleukin-1 alpha production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|cytometric bead array" EXACT [] -is_a: OBI:0001388 ! biological activity assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001748 name: ELISPOT assay measuring epitope specific interferon-beta production by T cells -def: "An assay of epitope specific interferon-beta production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|ELISPOT" EXACT [] -is_a: OBI:0001390 ! biological activity assay measuring epitope specific interferon-beta production by T cells +is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001749 name: intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells -def: "An assay of epitope specific interferon-beta production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|ICS" EXACT [] -is_a: OBI:0001390 ! biological activity assay measuring epitope specific interferon-beta production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells [Term] id: OBI:0001750 name: intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells -def: "An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|ICS" EXACT [] -is_a: OBI:0001600 ! biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells [Term] id: OBI:0001751 name: ELISA measuring epitope specific interferon-beta production by T cells -def: "An assay of epitope specific interferon-beta production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|ELISA" EXACT [] -is_a: OBI:0001390 ! biological activity assay measuring epitope specific interferon-beta production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells [Term] id: OBI:0001752 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells -def: "An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|RNA/DNA detection" EXACT [] -is_a: OBI:0001600 ! biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells [Term] id: OBI:0001753 name: ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells -def: "An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|ELISPOT" EXACT [] -is_a: OBI:0001600 ! biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001754 name: cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|cytometric bead array" EXACT [] -is_a: OBI:0001459 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001755 @@ -13226,93 +13529,106 @@ is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0001756 name: ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|ELISPOT" EXACT [] -is_a: OBI:0001459 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001757 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|RNA/DNA detection" EXACT [] -is_a: OBI:0001459 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells [Term] id: OBI:0001758 name: ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|ELISPOT" EXACT [] -is_a: OBI:0001345 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001759 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells." [] synonym: "CXCL12/SDF-1 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001776 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001776 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells [Term] id: OBI:0001760 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells." [] synonym: "CXCL13/BLC release|RNA/DNA detection" EXACT [] -is_a: OBI:0001779 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001779 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells [Term] id: OBI:0001761 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells -def: "An assay of epitope specific chemokine (C-X-C motif) ligand 16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells." [] synonym: "CXCL16 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001778 ! biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001778 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells [Term] id: OBI:0001762 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells." [] synonym: "CCL21/SLC release|RNA/DNA detection" EXACT [] -is_a: OBI:0001774 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001774 ! assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells [Term] id: OBI:0001763 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells." [] synonym: "CCL22/MDC release|RNA/DNA detection" EXACT [] -is_a: OBI:0001777 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001777 ! assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells [Term] id: OBI:0001764 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|cytometric bead array" EXACT [] -is_a: OBI:0001345 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001765 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|RNA/DNA detection" EXACT [] -is_a: OBI:0001345 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells [Term] id: OBI:0001766 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells -def: "An assay of epitope specific vascular endothelial growth factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|RNA/DNA detection" EXACT [] -is_a: OBI:0001570 ! biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells [Term] id: OBI:0001767 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 19 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells." [] synonym: "CCL19/MIP-3b release|RNA/DNA detection" EXACT [] -is_a: OBI:0001775 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001775 ! assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells [Term] id: OBI:0001768 name: intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|ICS" EXACT [] -is_a: OBI:0001276 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells [Term] id: OBI:0001769 @@ -13323,278 +13639,306 @@ is_a: OBI:0000202 ! investigation agent role [Term] id: OBI:0001770 name: intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells -def: "An assay of epitope specific vascular endothelial growth factor production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|ICS" EXACT [] -is_a: OBI:0001570 ! biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells [Term] id: OBI:0001771 name: ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells -def: "An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|ELISPOT" EXACT [] -is_a: OBI:0001570 ! biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001772 -name: biological activity assay measuring epitope specific interleukin-17F production by T cells +name: assay measuring epitope specific interleukin-17F production by T cells def: "An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production." [] synonym: "IL-17F release|biological activity" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001773 -name: biological activity assay measuring epitope specific interleukin-17A production by T cells +name: assay measuring epitope specific interleukin-17A production by T cells def: "An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production." [] synonym: "IL-17A release|biological activity" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001774 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells." [] synonym: "CCL21/SLC release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001775 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells." [] synonym: "CCL19/MIP-3b release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001776 -name: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells +name: assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells." [] synonym: "CXCL12/SDF-1 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001777 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells." [] synonym: "CCL22/MDC release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001778 -name: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells +name: assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells." [] synonym: "CXCL16 release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001779 -name: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells +name: assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells." [] synonym: "CXCL13/BLC release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001780 name: ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|ELISPOT" EXACT [] -is_a: OBI:0001333 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001781 name: cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|cytometric bead array" EXACT [] -is_a: OBI:0001456 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001782 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|RNA/DNA detection" EXACT [] -is_a: OBI:0001456 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells [Term] id: OBI:0001783 name: intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells -def: "An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|ICS" EXACT [] -is_a: OBI:0001465 ! biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells [Term] id: OBI:0001784 name: ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells -def: "An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|ELISPOT" EXACT [] -is_a: OBI:0001465 ! biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001785 name: intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|ICS" EXACT [] -is_a: OBI:0001456 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells [Term] id: OBI:0001786 name: ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|ELISPOT" EXACT [] -is_a: OBI:0001456 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001787 name: cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells -def: "An assay of epitope specific vascular endothelial growth factor production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|cytometric bead array" EXACT [] -is_a: OBI:0001570 ! biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001788 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|RNA/DNA detection" EXACT [] -is_a: OBI:0001400 ! biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001789 name: intracellular cytokine staining assay measuring epitope specific RANTES production by T cells -def: "An assay of epitope specific RANTES production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|ICS" EXACT [] -is_a: OBI:0001232 ! biological activity assay measuring epitope specific RANTES production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells [Term] id: OBI:0001790 name: ELISPOT assay measuring epitope specific RANTES production by T cells -def: "An assay of epitope specific RANTES production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|ELISPOT" EXACT [] -is_a: OBI:0001232 ! biological activity assay measuring epitope specific RANTES production by T cells +is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001791 name: ELISPOT assay measuring epitope specific lymphotoxin A production by T cells -def: "An assay of epitope specific lymphotoxin A production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|ELISPOT" EXACT [] is_a: OBI:0001272 ! ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001327 ! biological activity assay measuring epitope specific lymphotoxin A production by T cells +is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells [Term] id: OBI:0001792 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells -def: "An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|RNA/DNA detection" EXACT [] -is_a: OBI:0001333 ! biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells [Term] id: OBI:0001793 name: cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells -def: "An assay of epitope specific lymphotoxin A production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|cytometric bead array" EXACT [] -is_a: OBI:0001327 ! biological activity assay measuring epitope specific lymphotoxin A production by T cells +is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells is_a: OBI:0001368 ! cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001794 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells -def: "An assay of epitope specific lymphotoxin A production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|RNA/DNA detection" EXACT [] -is_a: OBI:0001327 ! biological activity assay measuring epitope specific lymphotoxin A production by T cells +is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells is_a: OBI:0001788 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001795 name: ELISPOT assay measuring epitope specific IP-10 production by T cells -def: "An assay of epitope specific IP-10 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|ELISPOT" EXACT [] -is_a: OBI:0001308 ! biological activity assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001796 name: intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells -def: "An assay of epitope specific IP-10 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|ICS" EXACT [] -is_a: OBI:0001308 ! biological activity assay measuring epitope specific IP-10 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells [Term] id: OBI:0001797 name: ELISPOT assay measuring epitope specific interleukin-9 production by T cells -def: "An assay of epitope specific interleukin-9 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|ELISPOT" EXACT [] -is_a: OBI:0001253 ! biological activity assay measuring interleukin-9 production by T cells +is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001798 name: intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells -def: "An assay of epitope specific interleukin-9 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|ICS" EXACT [] -is_a: OBI:0001253 ! biological activity assay measuring interleukin-9 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells [Term] id: OBI:0001799 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells -def: "An assay of epitope specific interleukin-9 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001253 ! biological activity assay measuring interleukin-9 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells [Term] id: OBI:0001800 name: ELISPOT assay measuring epitope specific interleukin-8 production by T cells -def: "An assay of epitope specific interleukin-8 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|ELISPOT" EXACT [] -is_a: OBI:0001218 ! biological activity assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001801 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells -def: "An assay of epitope specific interleukin-8 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001218 ! biological activity assay measuring epitope specific interleukin-8 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells [Term] id: OBI:0001802 name: ELISPOT assay measuring epitope specific interleukin-3 production by T cells -def: "An assay of epitope specific interleukin-3 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|ELISPOT" EXACT [] -is_a: OBI:0001406 ! biological activity assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001803 name: ELISA measuring epitope specific interleukin-7 production by T cells -def: "An assay of epitope specific interleukin-7 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|ELISA" EXACT [] -is_a: OBI:0001587 ! biological activity assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells [Term] id: OBI:0001804 name: ELISPOT assay measuring epitope specific interleukin-7 production by T cells -def: "An assay of epitope specific interleukin-7 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|ELISPOT" EXACT [] -is_a: OBI:0001587 ! biological activity assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001805 name: intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells -def: "An assay of epitope specific interleukin-7 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|ICS" EXACT [] -is_a: OBI:0001587 ! biological activity assay measuring epitope specific interleukin-7 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells [Term] id: OBI:0001806 name: intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells -def: "An assay of epitope specific interleukin-27 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|ICS" EXACT [] -is_a: OBI:0001198 ! biological activity assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells [Term] id: OBI:0001807 name: cytometric bead array assay measuring epitope specific interleukin-3 production by T cells -def: "An assay of epitope specific interleukin-3 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|cytometric bead array" EXACT [] -is_a: OBI:0001406 ! biological activity assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001808 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells -def: "An assay of epitope specific interleukin-3 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001406 ! biological activity assay measuring epitope specific interleukin-3 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001809 @@ -13613,37 +13957,42 @@ is_a: OBI:0001269 ! biological activity assay measuring epitope specific cytotox [Term] id: OBI:0001811 name: cytometric bead array assay measuring epitope specific interleukin-27 production by T cells -def: "An assay of epitope specific interleukin-27 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|cytometric bead array" EXACT [] -is_a: OBI:0001198 ! biological activity assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001812 name: intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells -def: "An assay of epitope specific interleukin-23 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|ICS" EXACT [] -is_a: OBI:0001363 ! biological activity assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells [Term] id: OBI:0001813 name: ELISPOT assay measuring epitope specific interleukin-27 production by T cells -def: "An assay of epitope specific interleukin-27 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|ELISPOT" EXACT [] -is_a: OBI:0001198 ! biological activity assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001814 name: ELISA measuring epitope specific interleukin-27 production by T cells -def: "An assay of epitope specific interleukin-27 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|ELISA" EXACT [] -is_a: OBI:0001198 ! biological activity assay measuring epitope specific interleukin-27 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells [Term] id: OBI:0001815 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells -def: "An assay of epitope specific interleukin-18 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001380 ! biological activity assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells [Term] id: OBI:0001816 @@ -13655,9 +14004,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001817 name: ELISPOT assay measuring epitope specific interleukin-18 production by T cells -def: "An assay of epitope specific interleukin-18 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|ELISPOT" EXACT [] -is_a: OBI:0001380 ! biological activity assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001818 @@ -13683,16 +14033,18 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001821 name: ELISPOT assay measuring epitope specific interleukin-22 production by T cells -def: "An assay of epitope specific interleukin-22 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|ELISPOT" EXACT [] -is_a: OBI:0001217 ! biological activity assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001822 name: ELISPOT assay measuring epitope specific interleukin-23 production by T cells -def: "An assay of epitope specific interleukin-23 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|ELISPOT" EXACT [] -is_a: OBI:0001363 ! biological activity assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001823 @@ -13704,9 +14056,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001824 name: intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells -def: "An assay of epitope specific interleukin-18 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|ICS" EXACT [] -is_a: OBI:0001380 ! biological activity assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells [Term] id: OBI:0001825 @@ -13718,62 +14071,66 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001826 name: ELISPOT assay measuring epitope specific interleukin-21 production by T cells -def: "An assay of epitope specific interleukin-21 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|ELISPOT" EXACT [] -is_a: OBI:0001237 ! biological activity assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001827 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001276 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells [Term] id: OBI:0001828 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|cytometric bead array" EXACT [] -is_a: OBI:0001276 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001829 name: ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|ELISPOT" EXACT [] -is_a: OBI:0001276 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001830 name: ELISPOT assay measuring epitope specific interleukin-17F production by T cells -def: "A T cell epitope specific interleukin-17F production assay that uses an ELISPOT." [] +def: "An enzyme-linked immunospot assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|ELISPOT" EXACT [] is_a: OBI:0001354 ! ELISPOT assay measuring epitope specific interleukin-17 production by T cells -is_a: OBI:0001772 ! biological activity assay measuring epitope specific interleukin-17F production by T cells +is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells [Term] id: OBI:0001831 name: ELISA measuring epitope specific interleukin-17F production by T cells -def: "A T cell epitope specific interleukin-17F production assay that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|ELISA" EXACT [] -is_a: OBI:0001772 ! biological activity assay measuring epitope specific interleukin-17F production by T cells +is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells is_a: OBI:1110162 ! ELISA measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001832 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells -def: "A T cell epitope specific interleukin-17F production assay that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|RNA/DNA detection" EXACT [] is_a: OBI:0001291 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells -is_a: OBI:0001772 ! biological activity assay measuring epitope specific interleukin-17F production by T cells +is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells [Term] id: OBI:0001833 name: ELISPOT assay measuring epitope specific interleukin-17A production by T cells -def: "A T cell epitope specific interleukin-17A production assay that uses an ELISPOT." [] +def: "An enzyme-linked immunospot assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|ELISPOT" EXACT [] is_a: OBI:0001354 ! ELISPOT assay measuring epitope specific interleukin-17 production by T cells -is_a: OBI:0001773 ! biological activity assay measuring epitope specific interleukin-17A production by T cells +is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells [Term] id: OBI:0001834 @@ -13784,87 +14141,98 @@ is_a: OBI:0000011 ! planned process [Term] id: OBI:0001835 name: cytometric bead array assay measuring epitope specific interleukin-18 production by T cells -def: "An assay of epitope specific interleukin-18 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|cytometric bead array" EXACT [] -is_a: OBI:0001380 ! biological activity assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001836 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells -def: "An assay of epitope specific interleukin-16 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001280 ! biological activity assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001837 name: ELISA measuring epitope specific interleukin-16 production by T cells -def: "An assay of epitope specific interleukin-16 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|ELISA" EXACT [] -is_a: OBI:0001280 ! biological activity assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001838 name: ELISPOT assay measuring epitope specific interleukin-16 production by T cells -def: "An assay of epitope specific interleukin-16 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|ELISPOT" EXACT [] -is_a: OBI:0001280 ! biological activity assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001839 name: intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells -def: "An assay of epitope specific interleukin-16 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|ICS" EXACT [] -is_a: OBI:0001280 ! biological activity assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001840 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells -def: "A T cell epitope specific interleukin-17A production assay that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|RNA/DNA detection" EXACT [] is_a: OBI:0001291 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells -is_a: OBI:0001773 ! biological activity assay measuring epitope specific interleukin-17A production by T cells +is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells [Term] id: OBI:0001841 name: intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells -def: "An assay of epitope specific interleukin-1 beta production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|ICS" EXACT [] -is_a: OBI:0001449 ! biological activity assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells [Term] id: OBI:0001842 name: ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells -def: "An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|ELISPOT" EXACT [] -is_a: OBI:0001449 ! biological activity assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001843 name: detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells -def: "An assay of epitope specific interleukin-15 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|RNA/DNA detection" EXACT [] -is_a: OBI:0001292 ! biological activity assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells [Term] id: OBI:0001844 name: ELISPOT assay measuring epitope specific interleukin-12 production by T cells -def: "An assay of epitope specific interleukin-12 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|ELISPOT" EXACT [] -is_a: OBI:0001391 ! biological activity assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001845 name: intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells -def: "An assay of epitope specific interleukin-15 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|ICS" EXACT [] -is_a: OBI:0001292 ! biological activity assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells [Term] id: OBI:0001846 name: ELISPOT assay measuring epitope specific interleukin-15 production by T cells -def: "An assay of epitope specific interleukin-15 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|ELISPOT" EXACT [] -is_a: OBI:0001292 ! biological activity assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001848 @@ -14380,6 +14748,7 @@ is_a: OBI:0001926 ! microRNA profiling assay id: OBI:0001923 name: protein sequencing by tandem mass spectrometry assay def: "A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation." [] +is_a: OBI:0000470 ! mass spectrometry assay is_a: OBI:0600047 ! sequencing assay [Term] @@ -14784,9 +15153,10 @@ is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001989 -name: purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection -def: "A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation." [] +name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex +def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|purified MHC/direct/radioactivity|nM" EXACT [] +is_a: OBI:0000201 ! radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] @@ -14801,14 +15171,14 @@ id: OBI:0001991 name: assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring half maximal effective concentration (EC50)." [] synonym: "half maximal effective concentration (EC50)|binding assay|nM" EXACT [] -is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex +is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001992 name: assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50)." [] synonym: "half maximal inhibitory concentration (IC50)|binding assay|nM" EXACT [] -is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex +is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001993 @@ -14827,38 +15197,42 @@ is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001995 name: chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium association constant (KA) determination assay that uses an analytical chromatography assay." [] +def: "An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|chromatography|1/nM" EXACT [] +is_a: OBI:0001630 ! analytical chromatography is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001996 name: chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses an analytical chromatography assay." [] +def: "An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|chromatography|nM" EXACT [] +is_a: OBI:0001630 ! analytical chromatography is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001997 name: hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex -def: "A footprinting assay that uses hydrogen/deuterium exchange to measure B cell epitope qualitative binding to antibody." [] +def: "A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|hydrogen/deuterium exchange footprinting assay" EXACT [] +is_a: OBI:0001976 ! hydrogen/deuterium exchange footprinting assay is_a: OBI:0002449 ! footprinting assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0001998 name: immunohistochemistry assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses an immunohistochemistry assay." [] +def: "A immunohistochemistry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|immunohistochemistry" EXACT [] is_a: OBI:0001652 ! immuno staining assay measuring binding of a B cell epitope:antibody complex +is_a: OBI:0001986 ! immunohistochemistry [Term] id: OBI:0001999 -name: 3D structure determining assay of a T cell epitope:MHC:TCR complex -def: "A T cell epitope recognition assay that uses a 3D structure determination of bound complex assay." [] +name: 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex +def: "A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex." [] synonym: "3D structure|any method" EXACT [] -is_a: OBI:0600045 ! 3D structure determination assay -is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex +is_a: OBI:0001145 ! 3D structure determination of bound molecular complex assay +is_a: OBI:0003128 ! T cell epitope assay [Term] id: OBI:0002000 @@ -15239,11 +15613,11 @@ is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002050 -name: 3D structure determining assay of a MHC:ligand complex -def: "A MHC:ligand binding assay that uses a 3D structure determination of bound complex assay." [] +name: 3D molecular structure determination assay of a MHC:ligand complex +def: "A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex." [] synonym: "3D structure|any method" EXACT [] -is_a: OBI:0001145 ! 3D structure determination of bound complex assay -is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex +is_a: OBI:0001145 ! 3D structure determination of bound molecular complex assay +is_a: OBI:0002075 ! MHC ligand assay [Term] id: OBI:0002051 @@ -15262,9 +15636,10 @@ is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection f [Term] id: OBI:0002053 name: microarray assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a microarray." [] +def: "A microarray assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|microarray" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex +is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0002054 @@ -15275,52 +15650,54 @@ is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell e [Term] id: OBI:0002055 -name: assay measuring T cell epitope specific biological activity -def: "A T cell epitope recognition assay that detects biological activity." [] +name: assay measuring biological activity resulting from T cell epitope:MHC:TCR binding +def: "A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope." [] synonym: "biological activity|any method" EXACT [] -is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex +is_a: OBI:0003128 ! T cell epitope assay [Term] id: OBI:0002056 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells def: "A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells." [] synonym: "CCL17/TARC release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002057 -name: biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells +name: assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells def: "A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells." [] synonym: "MIF release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002058 -name: biological activity assay measuring epitope specific oncostatin M production by T cells +name: assay measuring epitope specific oncostatin M production by T cells def: "A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells." [] synonym: "oncostatin M release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002059 name: assay measuring a binding constant of a T cell epitope:MHC:TCR complex def: "A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. " [] synonym: "binding constant|binding assay" EXACT [] -is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex +is_a: OBI:0003147 ! assay measuring quantitative binding of an epitope:MHC:TCR complex [Term] id: OBI:0002060 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay." [] +def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells." [] synonym: "CCL17/TARC release|RNA/DNA detection" EXACT [] -is_a: OBI:0002056 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0002056 ! assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells [Term] id: OBI:0002061 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 22 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells." [] synonym: "CCL22/MDC release|cytometric bead array" EXACT [] -is_a: OBI:0001777 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells +is_a: OBI:0001777 ! assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002062 @@ -15360,16 +15737,18 @@ is_a: OBI:0001436 ! biological activity assay measuring epitope specific granzym [Term] id: OBI:0002067 name: cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells -def: "An assay of epitope specific macrophage migration inhibitory factor (MIF) production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells." [] synonym: "MIF release|cytometric bead array" EXACT [] -is_a: OBI:0002057 ! biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells +is_a: OBI:0002057 ! assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002068 name: cytometric bead array assay measuring epitope specific oncostatin M production by T cells -def: "An assay of epitope specific oncostatin M production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects oncostatin M production by T cells." [] synonym: "oncostatin M release|cytometric bead array" EXACT [] -is_a: OBI:0002058 ! biological activity assay measuring epitope specific oncostatin M production by T cells +is_a: OBI:0002058 ! assay measuring epitope specific oncostatin M production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002069 @@ -15395,8 +15774,8 @@ is_a: OBI:1110131 ! biological activity assay measuring epitope specific prolife [Term] id: OBI:0002072 -name: assay measuring qualitiative binding of a MHC:ligand complex -def: "A MHC:ligand binding assay that detects qualitative binding." [] +name: assay measuring qualitative binding of a MHC:ligand complex +def: "An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output." [] synonym: "qualitative binding|binding assay" EXACT [] is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex @@ -15412,13 +15791,13 @@ id: OBI:0002074 name: in vitro assay measuring T cell epitope specific suppression def: "T cell epitope dependent biological activity assay that detects suppression of an in vitro response." [] synonym: "suppression|in vitro assay" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0002075 name: MHC ligand assay -def: "An immune epitope assay that detects either the processing and presentation of a ligand by an antigen presenting cell or the binding of a ligand to an MHC molecule." [] -synonym: "ligand presentation/binding|binding assay" EXACT [] +def: "An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule." [] +synonym: "MHC ligand assay|any method" EXACT [] is_a: OBI:1110128 ! immune epitope assay [Term] @@ -15595,36 +15974,41 @@ is_a: OBI:0002059 ! assay measuring a binding constant of a T cell epitope:MHC:T [Term] id: OBI:0002101 name: small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex -def: "A B cell epitope 3D structure determination assay that uses a small-angle X-ray scattering assay." [] +def: "A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex" [] synonym: "3D structure|small-angle scattering assay" EXACT [] -is_a: OBI:0001721 ! 3D structure determining assay of a 3D B cell epitope:antibody complex +is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex +is_a: OBI:0002108 ! small-angle scattering 3D molecular structure determination assay [Term] id: OBI:0002102 name: bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex -def: "A bio-layer interferometry assay that measures the on rate of a B cell epitope. " [] +def: "A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. " [] synonym: "on rate|bio-layer interferometry assay|M^-1s^-1" EXACT [] +is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002103 name: bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex -def: "A bio-layer interferometry assay that measures the off rate of a B cell epitope." [] +def: "A bio-layer interferometry assay that measures the off rate of an antigen with an antibody." [] synonym: "off rate|bio-layer interferometry assay|1/s" EXACT [] +is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002104 name: bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex -def: "A bio-layer interferometry assay that detects a B cell epitope qualitative binding to antibody." [] +def: "A bio-layer interferometry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|bio-layer interferometry assay" EXACT [] +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002105 name: bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A bio-layer interferometry assay that measures the dissociation constant [KD] of a B cell epitope binding. " [] +def: "A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. " [] synonym: "dissociation constant KD|bio-layer interferometry assay|nM" EXACT [] +is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] @@ -15643,10 +16027,10 @@ is_a: OBI:0001146 ! binding assay [Term] id: OBI:0002108 -name: small-angle scattering assay -def: "A 3D structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined." [] +name: small-angle scattering 3D molecular structure determination assay +def: "A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined." [] synonym: "SAXS" EXACT [] -is_a: OBI:0600045 ! 3D structure determination assay +is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0002109 @@ -15696,6 +16080,7 @@ id: OBI:0002115 name: cytometry time of flight assay def: "A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry." [] synonym: "CyTOF" EXACT [] +synonym: "mass cytometry assay" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] @@ -15815,16 +16200,17 @@ is_a: OBI:0000070 ! assay [Term] id: OBI:0002133 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells -def: "An assay of epitope specific chemokine (C-C motif) ligand 20 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells." [] synonym: "CCL20/MIP-3a release|cytometric bead array" EXACT [] -is_a: OBI:0002134 ! biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells +is_a: OBI:0002134 ! assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002134 -name: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells +name: assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells." [] synonym: "CCL20/MIP-3a release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002136 @@ -16850,10 +17236,10 @@ is_a: OBI:0000070 ! assay [Term] id: OBI:0002437 -name: widefield microscopy +name: widefield microscopy assay def: "A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated." [] synonym: "WFM" EXACT [] -is_a: CHMO:0000087 ! fluorescence microscopy +is_a: CHMO:0000087 ! fluorescence microscopy assay [Term] id: OBI:0002438 @@ -16930,30 +17316,33 @@ is_a: OBI:0000253 ! artificially induced nucleic acid hybridization [Term] id: OBI:0002449 name: footprinting assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a footprinting assay." [] +def: "A footprinting assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|footprinting assay" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex +is_a: OBI:0002162 ! footprinting assay [Term] id: OBI:0002450 name: hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex -def: "A footprinting assay that uses hydroxyl-radical footprinting to measure B cell epitope qualitative binding to antibody." [] +def: "A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|hydroxyl-radical footprinting assay" EXACT [] +is_a: OBI:0002442 ! hydroxyl-radical footprinting assay is_a: OBI:0002449 ! footprinting assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0002451 name: ELISA measuring epitope specific interferon-alpha production by T cells -def: "An assay of epitope specific interferon-alpha production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells." [] synonym: "IFNa release|ELISA" EXACT [] -is_a: OBI:0002452 ! biological activity assay measuring epitope specific interferon-alpha production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0002452 ! assay measuring epitope specific interferon-alpha production by T cells [Term] id: OBI:0002452 -name: biological activity assay measuring epitope specific interferon-alpha production by T cells +name: assay measuring epitope specific interferon-alpha production by T cells def: "A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells." [] synonym: "IFNa release|biological activity" EXACT [] -is_a: OBI:1110129 ! biological activity assay measuring epitope specific cytokine production by T cells +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002453 @@ -18015,7 +18404,7 @@ name: direct RNA sequencing assay def: "An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA." [] synonym: "direct RNA-seq" EXACT [] synonym: "DRS" EXACT [] -is_a: OBI:0001271 ! RNA-seq assay +is_a: OBI:0001177 ! RNA sequencing assay [Term] id: OBI:0002630 @@ -18252,16 +18641,18 @@ is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002664 name: cytometric bead array assay measuring epitope specific interleukin-15 production by T cells -def: "An assay of epitope specific interleukin-15 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|cytometric bead array" EXACT [] -is_a: OBI:0001292 ! biological activity assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002665 name: cytometric bead array assay measuring epitope specific interleukin-16 production by T cells -def: "An assay of epitope specific interleukin-16 production by T cells that uses a cytometric bead array assay." [] +def: "A cytometric bead array assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|cytometric bead array" EXACT [] -is_a: OBI:0001280 ! biological activity assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells +is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002666 @@ -18370,8 +18761,8 @@ is_a: OBI:0000436 ! needle id: OBI:0002680 name: pseudovirus entry assay def: "An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest." [] -synonym: " pseudotype cell entry" EXACT [] -synonym: " pseudotype entry" EXACT [] +synonym: "pseudotype cell entry" EXACT [] +synonym: "pseudotype entry" EXACT [] synonym: "pseudotyped particle cell entry assay" EXACT [] synonym: "pseudovirus cell entry" EXACT [] is_a: OBI:0001187 ! infectious agent detection assay @@ -18459,19 +18850,19 @@ is_a: OBI:0000070 ! assay id: OBI:0002693 name: restriction fragment length polymorphism assay def: "An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences." [] -synonym: " restriction fragment length polymorphism analysis" EXACT [] -synonym: " RFLP " EXACT [] -synonym: "restriction fragment length polymorphism " EXACT [] +synonym: "restriction fragment length polymorphism" EXACT [] +synonym: "restriction fragment length polymorphism analysis" EXACT [] +synonym: "RFLP" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002694 name: DNA fingerprinting assay def: "An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA." [] -synonym: " DNA finger printing" EXACT [] -synonym: " DNA fingerprint " EXACT [] -synonym: " DNA fingerprinting " EXACT [] -synonym: "DNA profiling " EXACT [] +synonym: "DNA finger printing" EXACT [] +synonym: "DNA fingerprint" EXACT [] +synonym: "DNA fingerprinting" EXACT [] +synonym: "DNA profiling" EXACT [] is_a: OBI:0000070 ! assay [Term] @@ -18520,8 +18911,8 @@ is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay id: OBI:0002701 name: insecticide resistance by detecting acetylcholinesterase activity assay def: "An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase." [] -synonym: " AChE activity assay" EXACT [] -synonym: "acetylcholinesterase assay " EXACT [] +synonym: "acetylcholinesterase assay" EXACT [] +synonym: "AChE activity assay" EXACT [] synonym: "AChE assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay @@ -18648,8 +19039,8 @@ is_a: OBI:0002709 ! insecticide resistance time response assay id: OBI:0002719 name: insecticide resistance by amplification refractory mutation system assay def: "An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations." [] -synonym: " ARMS" EXACT [] -synonym: "Amplification Refractory Mutation System " EXACT [] +synonym: "Amplification Refractory Mutation System" EXACT [] +synonym: "ARMS" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay @@ -18657,9 +19048,9 @@ is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay id: OBI:0002720 name: insecticide resistance by primer introduced restriction analysis PCR assay def: "An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes." [] -synonym: " PIRA-PCR " EXACT [] -synonym: " polymerase chain reaction-primer-introduced restriction analysis" EXACT [] -synonym: "Primer Introduced Restriction Analysis PCR " EXACT [] +synonym: "PIRA-PCR" EXACT [] +synonym: "polymerase chain reaction-primer-introduced restriction analysis" EXACT [] +synonym: "Primer Introduced Restriction Analysis PCR" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay @@ -18681,17 +19072,17 @@ is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay id: OBI:0002723 name: insecticide resistance by ligase detection reaction-fluorescent microsphere assay def: "An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction." [] -synonym: " ligase detection reaction-fluorescent microsphere assay" EXACT [] -synonym: "gene mutation detection by LDR-FMA " EXACT [] +synonym: "gene mutation detection by LDR-FMA" EXACT [] +synonym: "ligase detection reaction-fluorescent microsphere assay" EXACT [] is_a: OBI:0002722 ! insecticide resistance by ligase detection reaction assay [Term] id: OBI:0002724 name: insecticide resistance by PCR amplification of specific alleles assay def: "An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles." [] -synonym: " allele-specific amplification and amplification refractory mutation system" EXACT [] -synonym: " PCR amplification of specific alleles " EXACT [] -synonym: "PASA " EXACT [] +synonym: "allele-specific amplification and amplification refractory mutation system" EXACT [] +synonym: "PASA" EXACT [] +synonym: "PCR amplification of specific alleles" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay @@ -18757,8 +19148,8 @@ is_a: OBI:0000070 ! assay id: OBI:0002733 name: blood meal by counter current immunoelectrophoresis assay def: "A blood meal assay that uses a counter current immunoelectrophoresis technique." [] -synonym: " CIE" EXACT [] -synonym: "countercurrent immunoelectrophoresis " EXACT [] +synonym: "CIE" EXACT [] +synonym: "countercurrent immunoelectrophoresis" EXACT [] is_a: OBI:0002732 ! blood meal assay [Term] @@ -18892,7 +19283,7 @@ id: OBI:0002753 name: PRO-cap def: "Precision nuclear run-on and sequencing to detect Pol II initiation sites" [] synonym: "PRO-CAP" EXACT [] -is_a: OBI:0001271 ! RNA-seq assay +is_a: OBI:0001177 ! RNA sequencing assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] @@ -19019,6 +19410,18 @@ name: platelet-poor plasma preparation process def: "A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm." [] is_a: OBI:0600014 ! material component separation +[Term] +id: OBI:0002776 +name: cytometry analysis by automated gating +def: "A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest." [] +is_a: OBI:0200077 ! gating + +[Term] +id: OBI:0002777 +name: cytometry analysis by manual gating +def: "A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest." [] +is_a: OBI:0200077 ! gating + [Term] id: OBI:0002778 name: tracheal aspirate specimen @@ -19267,6 +19670,12 @@ name: specimen collection device def: "A container used to collect a specimen." [] is_a: OBI:0000968 ! device +[Term] +id: OBI:0002816 +name: chromatography vial +def: "A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography." [] +is_a: OBI:0000601 ! chromatography consumable + [Term] id: OBI:0002819 name: specimen pad @@ -19284,9 +19693,9 @@ is_a: OBI:0002814 ! specimen collection device id: OBI:0002820 name: specimen collection swab stick def: "A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material." [] -synonym: " sponge stick" EXACT [] synonym: "polyprobe" EXACT [] synonym: "sponge probe" EXACT [] +synonym: "sponge stick" EXACT [] synonym: "sponge-stick" EXACT [] is_a: OBI:0002814 ! specimen collection device @@ -19422,8 +19831,8 @@ is_a: OBI:0002904 ! adult arthropod specimen collection process id: OBI:0002913 name: arthropod specimen collection process def: "A specimen collection process that has the objective of collecting arthropods as specimens." [] -synonym: " field population catch" EXACT [] -synonym: "collection of arthropods " EXACT [] +synonym: "collection of arthropods" EXACT [] +synonym: "field population catch" EXACT [] is_a: OBI:0000659 ! specimen collection process [Term] @@ -19732,7 +20141,7 @@ is_a: OBI:0000615 ! protein expression profiling assay [Term] id: OBI:0002959 -name: tandem mass tag mass spectrometry +name: tandem mass tag mass spectrometry assay def: "A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins." [] is_a: OBI:0000470 ! mass spectrometry assay @@ -20493,98 +20902,1352 @@ def: "A population where the collection of individuals is located and maintained is_a: OBI:0000181 ! population [Term] -id: OBI:0003114 -name: Illumina MiniSeq -def: "A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run." [] -synonym: "MiniSeq" EXACT [] -is_a: OBI:0400103 ! DNA sequencer +id: OBI:0003087 +name: autofluorescence assay +def: "A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength." [] +synonym: "intrinsic fluorescence assay" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay [Term] -id: OBI:0005246 -name: injection function -def: "The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc." [] -is_a: BFO:0000034 ! function +id: OBI:0003088 +name: autofluorescence microscopy assay +def: "An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength." [] +is_a: OBI:0003087 ! autofluorescence assay [Term] -id: OBI:0100010 -name: Epstein Barr virus transformed B cell -def: "A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity" [] -is_a: OBI:0000047 ! processed material +id: OBI:0003089 +name: bulk assay for transposase-accessible chromatin using sequencing +def: "An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells." [] +synonym: "bulk ATAC-seq" EXACT [] +is_a: OBI:0002039 ! assay for transposase-accessible chromatin using sequencing [Term] -id: OBI:0100014 -name: chimera -def: "An organism which contains cells or tissues with a different genotype" [] -is_a: OBI:0100026 ! organism +id: OBI:0003090 +name: bulk RNA-seq assay +def: "An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells." [] +is_a: OBI:0001271 ! RNA-seq assay [Term] -id: OBI:0100015 -name: obsolete_anatomical entity -def: "An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true +id: OBI:0003091 +name: multiplexed fluorescent antibody imaging assay +def: "An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells." [] +is_a: OBI:0000185 ! imaging assay [Term] -id: OBI:0100016 -name: blood plasma specimen -def: "a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended." [] -synonym: "plasma" EXACT [] -is_a: OBI:0000953 ! processed specimen +id: OBI:0003092 +name: Cell DIVE multiplexed imaging assay +def: "A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section." [] +is_a: OBI:0003091 ! multiplexed fluorescent antibody imaging assay [Term] -id: OBI:0100017 -name: blood serum specimen -def: "A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors." [] -is_a: OBI:0000953 ! processed specimen +id: OBI:0003093 +name: co-detection by indexing assay +def: "A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels." [] +synonym: "CODEX" EXACT [] +is_a: OBI:0003091 ! multiplexed fluorescent antibody imaging assay [Term] -id: OBI:0100026 -name: organism -def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] -is_a: BFO:0000040 ! material entity +id: OBI:0003094 +name: fluorescence in-situ hybridization assay +def: "An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences." [] +synonym: "FISH" EXACT [] +is_a: OBI:0001686 ! in-situ hybridization assay [Term] -id: OBI:0100035 -name: obsolete_immortal cell -def: "a cell derived from a multicellular organism that has the potential to replicate indefinitely" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true +id: OBI:0003095 +name: decoding amplified targeted transcripts with fluorescence in situ hybridization assay +def: "A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types." [] +synonym: "DARTFISH" EXACT [] +is_a: OBI:0000424 ! transcription profiling assay +is_a: OBI:0003094 ! fluorescence in-situ hybridization assay [Term] -id: OBI:0100039 -name: obsolete_fragment derived from protein -def: "A material entity which is derived from a protein" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true +id: OBI:0003096 +name: imaging mass cytometry assay +def: "A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry." [] +synonym: "imaging CyTOF" EXACT [] +synonym: "IMC" EXACT [] +is_a: OBI:0002115 ! cytometry time of flight assay [Term] -id: OBI:0100046 -name: phosphate buffered saline solution -def: "Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic)." [] -synonym: "PBS buffer" EXACT [] -is_a: OBI:0302729 ! chemical solution +id: OBI:0003097 +name: liquid chromatography mass spectrometry assay +def: "A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance." [] +synonym: "LC-MS" EXACT [] +is_a: OBI:0000470 ! mass spectrometry assay [Term] -id: OBI:0100051 -name: specimen -def: "A material entity that has the specimen role." [] -is_a: BFO:0000040 ! material entity +id: OBI:0003098 +name: lightsheet fluorescence microscopy assay +def: "A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera." [] +is_a: CHMO:0000087 ! fluorescence microscopy assay [Term] -id: OBI:0100055 -name: obsolete_cell line cell -def: "A material entity that represents generations of a primary culture." [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true +id: OBI:0003099 +name: matrix assisted laser desorption ionization imaging mass spectrometry assay +def: "A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses." [] +synonym: "MALDI-IMS" EXACT [] +is_a: OBI:0000470 ! mass spectrometry assay [Term] -id: OBI:0100056 -name: obsolete_immortal cell line culture -def: "A cell line that is expected to be capable of indefinite propagation in an vitro culture." [] -synonym: "immortal cell line sample" EXACT [] -synonym: "permanent cell line" EXACT [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true +id: OBI:0003100 +name: multiplexed ion beam imaging assay +def: "A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry." [] +synonym: "MIBI" EXACT [] +is_a: OBI:0002115 ! cytometry time of flight assay + +[Term] +id: OBI:0003101 +name: nanospray desorption electrospray ionization assay +def: "A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray." [] +synonym: "NanoDESI" EXACT [] +is_a: OBI:0000470 ! mass spectrometry assay + +[Term] +id: OBI:0003102 +name: nanodroplet processing in one pot for trace samples assay +def: "A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression." [] +synonym: "NanoPOTS" EXACT [] +is_a: OBI:0000615 ! protein expression profiling assay + +[Term] +id: OBI:0003103 +name: periodic acid-Schiff staining assay +def: "A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components." [] +synonym: "PAS staining" EXACT [] +is_a: OBI:0600020 ! histological assay + +[Term] +id: OBI:0003104 +name: single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing +def: "An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation." [] +synonym: "sciATACseq" EXACT [] +is_a: OBI:0002039 ! assay for transposase-accessible chromatin using sequencing + +[Term] +id: OBI:0003105 +name: single-cell combinatorial indexing RNA sequencing assay +def: "A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation." [] +synonym: "sciRNAseq" EXACT [] +is_a: OBI:0002631 ! single-cell RNA sequencing assay + +[Term] +id: OBI:0003106 +name: sequential fluorescence in-situ hybridization assay +def: "A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved." [] +synonym: "seqFISH" EXACT [] +is_a: OBI:0003094 ! fluorescence in-situ hybridization assay + +[Term] +id: OBI:0003107 +name: slide-seq assay +def: "An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing." [] +is_a: OBI:0001271 ! RNA-seq assay + +[Term] +id: OBI:0003108 +name: single-nucleus chromatin accessibility and mRNA expression sequencing assay +def: "A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs." [] +synonym: "SNARE-seq" EXACT [] +synonym: "SNAREseq" EXACT [] +is_a: OBI:0003109 ! single-nucleus RNA sequencing assay + +[Term] +id: OBI:0003109 +name: single-nucleus RNA sequencing assay +def: "A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing." [] +synonym: "single nuclei RNA sequencing" EXACT [] +synonym: "snRNA-seq" EXACT [] +synonym: "sNuc-seq" EXACT [] +is_a: OBI:0001271 ! RNA-seq assay + +[Term] +id: OBI:0003110 +name: gas chromatography mass spectrometry assay +def: "A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds." [] +synonym: "GC-MS" EXACT [] +is_a: OBI:0000470 ! mass spectrometry assay + +[Term] +id: OBI:0003111 +name: SOMAscan assay +def: "An analyte assay that uses aptamers to detect protein analytes in serum. " [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003112 +name: Olink assay +def: "A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR." [] +is_a: OBI:0003113 ! proximity extension assay + +[Term] +id: OBI:0003113 +name: proximity extension assay +def: "An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex." [] +is_a: OBI:0000443 ! analyte assay +is_a: OBI:0002692 ! polymerase chain reaction assay + +[Term] +id: OBI:0003114 +name: Illumina MiniSeq +def: "A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run." [] +synonym: "MiniSeq" EXACT [] +is_a: OBI:0400103 ! DNA sequencer + +[Term] +id: OBI:0003115 +name: antigen detection by cytometric bead array assay +def: "A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest." [] +is_a: OBI:0000920 ! cytometric bead array assay + +[Term] +id: OBI:0003116 +name: antibody detection by cytometric bead array assay +def: "A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. " [] +is_a: OBI:0000920 ! cytometric bead array assay + +[Term] +id: OBI:0003117 +name: 3D molecular structure determination assay +def: "An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex." [] +is_a: OBI:0600045 ! 3D structure determination assay + +[Term] +id: OBI:0003118 +name: electron-microscopy 3D molecular structure determination assay +def: "A 3D molecular structure determination assay that uses electron microscopy imaging." [] +is_a: OBI:0003117 ! 3D molecular structure determination assay + +[Term] +id: OBI:0003119 +name: antigen:antibody complex +def: "A complex of molecular entitites which is the result of an antibody binding to an antigen." [] +is_a: COB:0000080 ! complex of molecular entities + +[Term] +id: OBI:0003120 +name: epitope:MHC:TCR complex +def: "A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex." [] +is_a: COB:0000080 ! complex of molecular entities + +[Term] +id: OBI:0003121 +name: MHC:ligand complex +def: "A complex of molecular entities which is the result of a MHC molecule binding with a ligand." [] +is_a: COB:0000080 ! complex of molecular entities + +[Term] +id: OBI:0003122 +name: 3D cell structure determination assay +def: "A 3D structure determination assay that determines the 3-dimensional configuration of a cell." [] +is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0600045 ! 3D structure determination assay + +[Term] +id: OBI:0003123 +name: 3D neural cell structure determination assay +def: "A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell." [] +is_a: OBI:0003122 ! 3D cell structure determination assay + +[Term] +id: OBI:0003124 +name: neuron morphology assay +def: "A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron." [] +is_a: OBI:0003123 ! 3D neural cell structure determination assay + +[Term] +id: OBI:0003125 +name: mosaicism with repeat frameshift genetic sparse labeling +def: "A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons." [] +synonym: "MORF genetic sparse labeling" EXACT [] +is_a: OBI:0003123 ! 3D neural cell structure determination assay + +[Term] +id: OBI:0003126 +name: neuron morphology reconstruction assay +def: "A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST)." [] +is_a: OBI:0003124 ! neuron morphology assay + +[Term] +id: OBI:0003127 +name: B cell epitope assay +def: "An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope." [] +synonym: "B cell assay|any method" EXACT [] +is_a: OBI:1110128 ! immune epitope assay + +[Term] +id: OBI:0003128 +name: T cell epitope assay +def: "An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope." [] +synonym: "T cell assay|any method" EXACT [] +is_a: OBI:1110128 ! immune epitope assay + +[Term] +id: OBI:0003129 +name: chemical mutagenesis +def: "A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen." [] +is_a: OBI:0002620 ! random mutagenesis + +[Term] +id: OBI:0003130 +name: irradiation mutagenesis +def: "A form of random mutagenesis that produces a random mutation by exposing the organism to radiation." [] +synonym: "radiation induced mutagenesis" EXACT [] +is_a: OBI:0002620 ! random mutagenesis + +[Term] +id: OBI:0003131 +name: directed mutagenesis +def: "An induced mutation in which a specific gene(s) or part of a gene(s) is altered." [] +is_a: OBI:0001154 ! induced mutagenesis + +[Term] +id: OBI:0003132 +name: endonuclease mediated mutagenesis +def: "A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene." [] +is_a: OBI:0003131 ! directed mutagenesis + +[Term] +id: OBI:0003133 +name: cas mediated mutagenesis +def: "An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome." [] +synonym: "CRISPR mediated mutagenesis" EXACT [] +synonym: "CRISPR/cas mediated mutagenesis" EXACT [] +is_a: OBI:0003132 ! endonuclease mediated mutagenesis + +[Term] +id: OBI:0003134 +name: TALEN mediated mutagenesis +def: "An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome." [] +is_a: OBI:0003132 ! endonuclease mediated mutagenesis + +[Term] +id: OBI:0003135 +name: zinc finger mediated mutagenesis +def: "An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome." [] +synonym: "ZFN mediated mutagenesis" EXACT [] +is_a: OBI:0003132 ! endonuclease mediated mutagenesis + +[Term] +id: OBI:0003136 +name: transgenic mutagenesis +def: "A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion." [] +is_a: OBI:0002620 ! random mutagenesis + +[Term] +id: OBI:0003137 +name: gene-trap mutagenesis +def: "A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism." [] +is_a: OBI:0003136 ! transgenic mutagenesis + +[Term] +id: OBI:0003138 +name: enhancer-trap mutagenesis +def: "A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression." [] +is_a: OBI:0003136 ! transgenic mutagenesis + +[Term] +id: OBI:0003139 +name: targeted mutagenesis +def: "A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination." [] +synonym: "gene targeting by homologous recombination" EXACT [] +is_a: OBI:0003131 ! directed mutagenesis + +[Term] +id: OBI:0003140 +name: transposon-induced mutagenesis +def: "A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation." [] +is_a: OBI:0002620 ! random mutagenesis + +[Term] +id: OBI:0003141 +name: categorical binding datum +def: "A binding datum that is expressed as a categorical value." [] +synonym: "qualitative binding datum" EXACT [] +is_a: OBI:0001181 ! binding datum + +[Term] +id: OBI:0003142 +name: quantitative binding datum +def: "A binding datum that is expressed using numbers." [] +is_a: OBI:0001181 ! binding datum + +[Term] +id: OBI:0003143 +name: EC50 binding datum +def: "A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50)." [] +is_a: OBI:0001180 ! half maximal effective concentration (EC50) +is_a: OBI:0003142 ! quantitative binding datum + +[Term] +id: OBI:0003144 +name: IC50 binding datum +def: "A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50)." [] +is_a: OBI:0001191 ! half maximal inhibitory concentration (IC50) +is_a: OBI:0003142 ! quantitative binding datum + +[Term] +id: OBI:0003145 +name: assay measuring quantitative binding of a MHC:ligand complex +def: "An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output." [] +synonym: "quantitative binding|binding assay" EXACT [] +is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex + +[Term] +id: OBI:0003146 +name: assay measuring quantitative binding of an antigen:antibody complex +def: "An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output." [] +synonym: "quantitative binding|binding assay" EXACT [] +is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex + +[Term] +id: OBI:0003147 +name: assay measuring quantitative binding of an epitope:MHC:TCR complex +def: "An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output." [] +synonym: "quantitative binding|binding assay" EXACT [] +is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex + +[Term] +id: OBI:0003148 +name: albumin concentration assay +def: "An albumin assay that measures the concentration of albumin in a specimen." [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:0003149 +name: basophil percentage assay +def: "A basophil assay that measures the percentage of basophils in a specimen." [] +is_a: OBI:0003021 ! basophil assay + +[Term] +id: OBI:0003150 +name: calcium cation concentration assay +def: "A calcium cation assay that measures the concentration of calcium cations in a specimen." [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:0003151 +name: chloride concentration assay +def: "A chloride assay that measures the concentration of chloride in a specimen." [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:0003152 +name: cholesterol concentration assay +def: "A cholesterol assay that measures the concentration of cholesterol in a specimen." [] +is_a: OBI:2100031 ! cholesterol assay + +[Term] +id: OBI:0003153 +name: creatinine concentration assay +def: "A creatinine assay that measures the concentration of creatinine in a specimen." [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:0003154 +name: eosinophil percentage assay +def: "An eosinophil assay that measures the percentage of eosinophils in a specimen." [] +is_a: OBI:0003023 ! eosinophil assay + +[Term] +id: OBI:0003155 +name: globulin concentration assay +def: "A globulin assay that measures the concentration of globulin in a specimen." [] +is_a: OBI:0003015 ! globulin assay + +[Term] +id: OBI:0003156 +name: hemoglobin concentration assay +def: "A hemoglobin assay that measures the amount of hemoglobin in a specimen." [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:0003157 +name: high-density lipoprotein cholesterol concentration assay +def: "A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen." [] +is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay + +[Term] +id: OBI:0003158 +name: iron concentration assay +def: "An iron assay that measures the concentration of iron cation in a specimen." [] +is_a: OBI:0003011 ! iron assay + +[Term] +id: OBI:0003159 +name: low-density lipoprotein cholesterol concentration assay +def: "A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen." [] +is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay + +[Term] +id: OBI:0003160 +name: lymphocyte percentage assay +def: "A lymphocyte assay that measures the percentage of lymphocytes in a specimen." [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:0003161 +name: metamyelocyte count assay +def: "A metamyelocyte assay that measures the number of metamyelocytes in a specimen." [] +is_a: OBI:0003017 ! metamyelocyte assay + +[Term] +id: OBI:0003162 +name: metamyelocyte percentage assay +def: "A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen." [] +is_a: OBI:0003017 ! metamyelocyte assay + +[Term] +id: OBI:0003163 +name: methemoglobin percentage assay +def: "A methemoglobin assay that measures the percentage of methemoglobin in a specimen." [] +is_a: OBI:2100040 ! methemoglobin assay + +[Term] +id: OBI:0003164 +name: monocyte percentage assay +def: "A monocyte assay that measures the percentage of monocytes in a specimen." [] +is_a: OBI:0003025 ! monocyte assay + +[Term] +id: OBI:0003165 +name: myelocyte count assay +def: "A myelocyte assay that measures the number of myelocytes in a specimen." [] +is_a: OBI:0003016 ! myelocyte assay + +[Term] +id: OBI:0003166 +name: neutrophil percentage assay +def: "A neutrophil assay that measures the percentage of neutrophils in a specimen." [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:0003167 +name: phosphate ion concentration assay +def: "A phosphate ion assay that measures the concentration of phosphate ions in a specimen." [] +is_a: OBI:2100015 ! phosphate ion assay + +[Term] +id: OBI:0003168 +name: potassium(1+) concentration assay +def: "A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen." [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:0003170 +name: reticulocyte percentage assay +def: "A reticulocyte assay that measures the percentage of reticulocytes in a specimen." [] +is_a: OBI:0003026 ! reticulocyte assay + +[Term] +id: OBI:0003171 +name: sodium(1+) concentration assay +def: "A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen." [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:0003172 +name: thyroid stimulating hormone concentration assay +def: "A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen." [] +is_a: OBI:2100033 ! thyroid stimulating hormone assay + +[Term] +id: OBI:0003173 +name: triglyceride concentration assay +def: "A triglyceride assay that measures the concentration of triglycerides in a specimen." [] +is_a: OBI:2100029 ! triglyceride assay + +[Term] +id: OBI:0003174 +name: 3,3',5'-triiodothyronine concentration assay +def: "A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen." [] +is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay + +[Term] +id: OBI:0003175 +name: fibrinogen concentration assay +def: "A fibrinogen assay that measures the concentration of fibrinogen in a specimen." [] +is_a: OBI:0003010 ! fibrinogen assay + +[Term] +id: OBI:0003176 +name: free thyroxine concentration assay +def: "A thyroxine assay that measures the concentration of free thyroxine in a specimen." [] +is_a: OBI:2100035 ! thyroxine assay + +[Term] +id: OBI:0003177 +name: total thyroxine concentration assay +def: "A thyroxine assay that measures the concentration of total thyroxine in a specimen." [] +is_a: OBI:2100035 ! thyroxine assay + +[Term] +id: OBI:0003180 +name: direct bilirubin concentration assay +def: "A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen." [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:0003181 +name: indirect bilirubin concentration assay +def: "A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen." [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:0003182 +name: total bilirubin concentration assay +def: "A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen." [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:0003183 +name: mean cell hemoglobin assay +def: "A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes." [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:0003184 +name: mean cell hemoglobin concentration assay +def: "A hemoglobin assay that measures the concentration of hemoglobin in a specimen." [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:0003185 +name: mean platelet volume assay +def: "A platelet assay that measures the average volume of platelets in a specimen." [] +is_a: OBI:0003028 ! platelet assay + +[Term] +id: OBI:0003186 +name: immature neutrophil count assay +def: "A neutrophil assay that measures the number of immature neutrophils in a specimen." [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:0003187 +name: immature neutrophil percentage assay +def: "An neutrophil assay that measures the percentage of immature neutrophils in a specimen." [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:0003188 +name: nucleated erythrocyte percentage assay +def: "An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen." [] +is_a: OBI:0003190 ! erythrocyte assay + +[Term] +id: OBI:0003189 +name: mean cell volume assay +def: "An erythrocyte assay that measures the average volume of erythrocytes in a specimen." [] +is_a: OBI:0003190 ! erythrocyte assay + +[Term] +id: OBI:0003190 +name: erythrocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of erythrocytes." [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:0003191 +name: manual hematocrit assay +def: "A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes." [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:0003192 +name: adiponectin assay +def: "An analyte assay that measures the abundance of adiponectin" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:0003193 +name: adiponectin concentration assay +def: "An adiponectin assay that measures the concentration of adiponectin in a specimen." [] +is_a: OBI:0003192 ! adiponectin assay + +[Term] +id: OBI:0003194 +name: creatine assay +def: "An analyte assay that measures the abundance of creatine" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003195 +name: creatine concentration assay +def: "A creatine assay that measures the concentration of creatine in a specimen." [] +is_a: OBI:0003194 ! creatine assay + +[Term] +id: OBI:0003196 +name: estradiol assay +def: "An analyte assay that measures the abundance of estradiol" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003197 +name: estradiol concentration assay +def: "An estradiol assay that measures the concentration of estradiol in a specimen." [] +is_a: OBI:0003196 ! estradiol assay + +[Term] +id: OBI:0003202 +name: leptin assay +def: "An analyte assay that measures the abundance of leptin" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:0003203 +name: leptin concentration assay +def: "An leptin assay that measures the concentration of leptin in a specimen." [] +is_a: OBI:0003202 ! leptin assay + +[Term] +id: OBI:0003204 +name: lipoprotein concentration assay +def: "An analyte assay that measures the abundance of lipoprotein" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003205 +name: high-density lipoprotein concentration assay +def: "A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen." [] +is_a: OBI:0003204 ! lipoprotein concentration assay + +[Term] +id: OBI:0003206 +name: low-density lipoprotein concentration assay +def: "A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen." [] +is_a: OBI:0003204 ! lipoprotein concentration assay + +[Term] +id: OBI:0003207 +name: very-low-density lipoprotein concentration assay +def: "A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen." [] +is_a: OBI:0003204 ! lipoprotein concentration assay + +[Term] +id: OBI:0003208 +name: luteinizing hormone assay +def: "An analyte assay that measures the abundance of luteinizing hormone" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003209 +name: luteinizing hormone concentration assay +def: "A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen." [] +is_a: OBI:0003208 ! luteinizing hormone assay + +[Term] +id: OBI:0003210 +name: nitrite assay +def: "An analyte assay that measures the abundance of nitrite" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003211 +name: nitrite concentration assay +def: "A nitrite assay that measures the concentration of nitrite in a specimen." [] +is_a: OBI:0003210 ! nitrite assay + +[Term] +id: OBI:0003212 +name: phospholipid assay +def: "An analyte assay that measures the abundance of phospholipid" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003213 +name: phospholipid concentration assay +def: "A phospholipid assay that measures the concentration of phospholipids in a specimen." [] +is_a: OBI:0003212 ! phospholipid assay + +[Term] +id: OBI:0003214 +name: progesterone assay +def: "An analyte assay that measures the abundance of progesterone" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003215 +name: progesterone concentration assay +def: "A progesterone assay that measures the concentration of progesterone in a specimen." [] +is_a: OBI:0003214 ! progesterone assay + +[Term] +id: OBI:0003216 +name: testosterone assay +def: "An analyte assay that measures the abundance of testosterone" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003217 +name: testosterone concentration assay +def: "A testosterone assay that measures the concentration of testosterone in a specimen." [] +is_a: OBI:0003216 ! testosterone assay + +[Term] +id: OBI:0003218 +name: bile salt assay +def: "An analyte assay that measures the abundance of bile salt" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003219 +name: bile salt concentration assay +def: "A bile salt assay that measures the concentration of bile salt in a specimen." [] +is_a: OBI:0003218 ! bile salt assay + +[Term] +id: OBI:0003220 +name: fatty acid assay +def: "An analyte assay that measures the abundance of fatty acid" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003221 +name: free fatty acid concentration assay +def: "A fatty acid assay that measures the concentration of free fatty acids in a specimen." [] +is_a: OBI:0003220 ! fatty acid assay + +[Term] +id: OBI:0003222 +name: insulin assay +def: "An analyte assay that measures the abundance of insulin" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003223 +name: insulin concentration assay +def: "A insulin assay that measures the concentration of insulin in a specimen." [] +is_a: OBI:0003222 ! insulin assay + +[Term] +id: OBI:0003224 +name: follicle stimulating hormone assay +def: "An analyte assay that measures the abundance of follicle stimulating hormone" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003225 +name: follicle stimulating hormone concentration assay +def: "A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen." [] +is_a: OBI:0003224 ! follicle stimulating hormone assay + +[Term] +id: OBI:0003226 +name: total lymphocyte count assay +def: "A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen." [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:0003227 +name: total lymphocyte percentage assay +def: "A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen." [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:0003228 +name: fluorescent immunospot assay +def: "A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies." [] +synonym: "FLUOROSPOT" EXACT [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003229 +name: plasma proteomics assay +def: "A proteomics profiling assay that detects proteins in a blood plasma specimen." [] +is_a: OBI:0001318 ! proteomic profiling by array assay + +[Term] +id: OBI:0003230 +name: T cell activation induced marker assay +def: "A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers." [] +is_a: OBI:0000916 ! flow cytometry assay + +[Term] +id: OBI:0003231 +name: leukapheresis +def: "A blood harvesting process in which white blood cells are separated from a blood specimen." [] +is_a: OBI:1110095 ! blood harvesting + +[Term] +id: OBI:0003232 +name: cerebrospinal fluid assay +def: "An assay that has a cerebrospinal fluid specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003233 +name: endotracheal aspirate assay +def: "An assay that has an endotracheal aspirate specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003234 +name: induced sputum assay +def: "An assay that has an induced sputum specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003235 +name: lung assay +def: "An assay that has a lung specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003236 +name: milk assay +def: "An assay that has a milk specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003237 +name: feces assay +def: "An assay that has a feces specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003238 +name: umbilical cord blood assay +def: "An assay that has an umbilical cord blood specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003239 +name: saliva assay +def: "An assay that has a saliva specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003240 +name: cerebrospinal fluid microbiology assay +def: "An organism identification assay that has a cerebrospinal fluid specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003241 +name: endotracheal tube aspirate microbiology assay +def: "An organism identification assay that has an endotracheal aspirate specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003242 +name: induced sputum microbiology assay +def: "An organism identification assay that has an induced sputum specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003243 +name: blood assay datum +def: "A data item that is the specified output of a blood assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003244 +name: blood microbiology datum +def: "An organism identification assay that is the specified output of a blood microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003245 +name: feces assay datum +def: "A data item that is the specified output of a feces assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003246 +name: feces microbiology datum +def: "An organism identification assay that is the specified output of a feces microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003247 +name: urine assay datum +def: "A data item that is the specified output of a urine assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003248 +name: urine microbiology datum +def: "An organism identification assay that is the specified output of a urine microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003249 +name: induced sputum assay datum +def: "A data item that is the specified output of a induced sputum assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003251 +name: induced sputum microbiology datum +def: "An organism identification assay that is the specified output of an induced sputum microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003252 +name: cerebrospinal fluid assay datum +def: "A data item that is the specified output of a cerebrospinal fluid assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003253 +name: cerebrospinal fluid microbiology datum +def: "An organism identification assay that is the specified output of a cerebrospinal fluid microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003254 +name: endotracheal aspirate assay datum +def: "An organism identification assay that is the specified output of an endotracheal aspirate assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003255 +name: endotracheal tube aspirate microbiology datum +def: "An organism identification assay that is the specified output of an endotracheal tube aspirate microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003256 +name: lung microbiology datum +def: "An organism identification assay that is the specified output of a lung microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003257 +name: nasopharyngeal or oropharyngeal swab microbiology datum +def: "An organism identification assay that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003258 +name: pleural fluid microbiology datum +def: "An organism identification assay that is the specified output of a pleural fluid microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003259 +name: umbilical cord blood assay datum +def: "An organism identification assay that is the specified output of an umbilical cord blood assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003260 +name: umbilical cord blood microbiology datum +def: "An organism identification assay that is the specified output of an umbilical cord blood microbiology assay." [] +is_a: OBI:0003064 ! organism identification datum + +[Term] +id: OBI:0003261 +name: bacteria in blood datum +def: "A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003244 ! blood microbiology datum + +[Term] +id: OBI:0003262 +name: virus in blood datum +def: "A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003244 ! blood microbiology datum + +[Term] +id: OBI:0003263 +name: eukaryota in blood datum +def: "A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003244 ! blood microbiology datum + +[Term] +id: OBI:0003264 +name: bacteria in feces datum +def: "A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003246 ! feces microbiology datum + +[Term] +id: OBI:0003265 +name: eukaryota in feces datum +def: "A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003246 ! feces microbiology datum + +[Term] +id: OBI:0003266 +name: virus in feces datum +def: "A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003246 ! feces microbiology datum + +[Term] +id: OBI:0003267 +name: eukaryota in urine datum +def: "A urine microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003248 ! urine microbiology datum + +[Term] +id: OBI:0003268 +name: bacteria in induced sputum datum +def: "A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003251 ! induced sputum microbiology datum + +[Term] +id: OBI:0003269 +name: eukaryota in induced sputum datum +def: "A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003251 ! induced sputum microbiology datum + +[Term] +id: OBI:0003270 +name: virus in induced sputum datum +def: "A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003251 ! induced sputum microbiology datum + +[Term] +id: OBI:0003271 +name: bacteria in endotracheal tube aspirate datum +def: "A endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003255 ! endotracheal tube aspirate microbiology datum + +[Term] +id: OBI:0003272 +name: bacteria in lung datum +def: "A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003256 ! lung microbiology datum + +[Term] +id: OBI:0003273 +name: eukaryota in lung datum +def: "A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003256 ! lung microbiology datum + +[Term] +id: OBI:0003274 +name: virus in lung datum +def: "A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003256 ! lung microbiology datum + +[Term] +id: OBI:0003275 +name: bacteria in nasopharyngeal or oropharyngeal swab datum +def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum + +[Term] +id: OBI:0003276 +name: eukaryota in nasopharyngeal or oropharyngeal swab datum +def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum + +[Term] +id: OBI:0003277 +name: virus in nasopharyngeal or oropharyngeal swab datum +def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum + +[Term] +id: OBI:0003278 +name: bacteria in pleural fluid datum +def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003258 ! pleural fluid microbiology datum + +[Term] +id: OBI:0003279 +name: eukaryota in pleural fluid datum +def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003258 ! pleural fluid microbiology datum + +[Term] +id: OBI:0003280 +name: virus in pleural fluid datum +def: "A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003258 ! pleural fluid microbiology datum + +[Term] +id: OBI:0003281 +name: eukaryota in umbilical cord blood datum +def: "A umbilical cord blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen." [] +is_a: OBI:0003260 ! umbilical cord blood microbiology datum + +[Term] +id: OBI:0003282 +name: lung microbiology assay +def: "An organism identification assay that has a lung specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003283 +name: pleural fluid microbiology assay +def: "An organism identification assay that has a pleural fluid specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003284 +name: umbilical cord blood microbiology assay +def: "An organism identification assay that has an umbilical cord blood specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003285 +name: nasopharyngeal or oropharyngeal swab microbiology assay +def: "An organism identification assay that has a nasopharyngeal or oropharyngeal swab specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003286 +name: urine microbiology assay +def: "An organism identification assay that has a urine specimen as evaluant." [] +is_a: OBI:0001624 ! organism identification assay +is_a: OBI:0003043 ! urine assay + +[Term] +id: OBI:0003287 +name: multiplex real time polymerase chain reaction assay +def: "A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle." [] +synonym: "multiplexed real time polymerase chain reaction assay" EXACT [] +is_a: OBI:0000893 ! real time polymerase chain reaction assay + +[Term] +id: OBI:0003288 +name: multiplex real time reverse-transcription polymerase chain reaction assay +def: "A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle." [] +synonym: "multiplexed real time reverse-transcription polymerase chain reaction assay" EXACT [] +is_a: OBI:0000911 ! real time reverse-transcription polymerase chain reaction assay + +[Term] +id: OBI:0003289 +name: mosquito membrane feeding device +def: "A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0003290 +name: mosquito membrane feeding assay +def: "An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003291 +name: in silico design +def: "A study design that is executed primarily on a computer." [] +is_a: OBI:0500000 ! study design + +[Term] +id: OBI:0003292 +name: cytometric bead array assay measuring epitope specific granulysin release by T cells +def: "A cytometric bead array assay that detects granulysin release by T cells." [] +synonym: "granulysin release|cytometric bead array" EXACT [] +is_a: OBI:0001810 ! biological activity assay measuring epitope specific granulysin release by T cells + +[Term] +id: OBI:0003293 +name: cytometric bead array assay measuring epitope specific perforin release by T cells +def: "A cytometric bead array assay that detects perforin release by T cells." [] +synonym: "perforin release|cytometric bead array" EXACT [] +is_a: OBI:0001497 ! biological activity assay measuring epitope specific perforin release by T cells + +[Term] +id: OBI:0003294 +name: modified acid-fast stain microscopy assay +def: "A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating." [] +is_a: OBI:0002119 ! microscopy assay + +[Term] +id: OBI:0003295 +name: positive binding datum +def: "A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex." [] +is_a: OBI:0003141 ! categorical binding datum + +[Term] +id: OBI:0003296 +name: antibodies from lymphocyte secretions assay +def: "An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells." [] +synonym: "ALS assay" EXACT [] +synonym: "antibodies from lymphocyte supernatant assay" EXACT [] +is_a: OBI:0003040 ! blood assay + +[Term] +id: OBI:0005246 +name: injection function +def: "The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc." [] +is_a: BFO:0000034 ! function + +[Term] +id: OBI:0100010 +name: Epstein Barr virus transformed B cell +def: "A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity" [] +is_a: OBI:0000047 ! processed material + +[Term] +id: OBI:0100014 +name: chimera +def: "An organism which contains cells or tissues with a different genotype" [] +is_a: OBI:0100026 ! organism + +[Term] +id: OBI:0100015 +name: obsolete_anatomical entity +def: "An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'" [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: OBI:0100016 +name: blood plasma specimen +def: "a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended." [] +synonym: "plasma" EXACT [] +is_a: OBI:0000953 ! processed specimen + +[Term] +id: OBI:0100017 +name: blood serum specimen +def: "A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors." [] +is_a: OBI:0000953 ! processed specimen + +[Term] +id: OBI:0100026 +name: organism +def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] +is_a: BFO:0000040 ! material entity + +[Term] +id: OBI:0100035 +name: obsolete_immortal cell +def: "a cell derived from a multicellular organism that has the potential to replicate indefinitely" [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: OBI:0100039 +name: obsolete_fragment derived from protein +def: "A material entity which is derived from a protein" [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: OBI:0100046 +name: phosphate buffered saline solution +def: "Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic)." [] +synonym: "PBS buffer" EXACT [] +is_a: OBI:0302729 ! chemical solution + +[Term] +id: OBI:0100051 +name: specimen +def: "A material entity that has the specimen role." [] +is_a: BFO:0000040 ! material entity + +[Term] +id: OBI:0100055 +name: obsolete_cell line cell +def: "A material entity that represents generations of a primary culture." [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: OBI:0100056 +name: obsolete_immortal cell line culture +def: "A cell line that is expected to be capable of indefinite propagation in an vitro culture." [] +synonym: "immortal cell line sample" EXACT [] +synonym: "permanent cell line" EXACT [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true replaced_by: CLO:0009828 [Term] @@ -23649,9 +25312,10 @@ is_a: OGMS:0000063 ! disease course [Term] id: OBI:1110013 name: ELISPOT assay measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|ELISPOT" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110014 @@ -23782,9 +25446,9 @@ is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110037 name: assay measuring binding of a T cell epitope:MHC:TCR complex -def: "An immune epitope assay that detects T cell epitope recognition." [] +def: "A T cell epitope assay that measures the binding of T cell receptor to an epitope." [] synonym: "T cell binding|any method" EXACT [] -is_a: OBI:1110128 ! immune epitope assay +is_a: OBI:0003128 ! T cell epitope assay [Term] id: OBI:1110038 @@ -23917,9 +25581,10 @@ is_a: OBI:1110014 ! epitope binding by adaptive immune receptor [Term] id: OBI:1110059 name: ELISPOT assay measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|ELISPOT" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110061 @@ -24068,8 +25733,8 @@ is_a: GO:0008150 ! biological_process [Term] id: OBI:1110124 -name: assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex -def: "A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR." [] +name: assay measuring qualitative binding of a T cell epitope:MHC:TCR complex +def: "An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output." [] synonym: "qualitative binding|binding assay" EXACT [] is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex @@ -24084,43 +25749,43 @@ is_a: OBI:0002075 ! MHC ligand assay id: OBI:1110126 name: assay measuring binding of a MHC:ligand complex def: "A MHC ligand assay that detects the binding of a ligand to an MHC molecule." [] -synonym: "MHC binding|binding assay" EXACT [] +synonym: "MHC binding|any method" EXACT [] is_a: OBI:0002075 ! MHC ligand assay [Term] id: OBI:1110127 name: assay measuring binding of a B cell epitope:antibody complex -def: "An immune epitope assay that detects B cell epitope recognition." [] +def: "A B cell epitope assay that measures the binding of an antibody receptor to an epitope." [] synonym: "antibody binding|any method" EXACT [] -is_a: OBI:1110128 ! immune epitope assay +is_a: OBI:0003127 ! B cell epitope assay [Term] id: OBI:1110128 name: immune epitope assay -def: "An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event" [] +def: "An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event." [] synonym: "immune epitope assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:1110129 -name: biological activity assay measuring epitope specific cytokine production by T cells -def: "A T cell epitope dependent biological activity assay that detects cytokine production." [] +name: assay measuring epitope specific cytokine production by T cells +def: "A T cell epitope assay that detects cytokine production by T cells." [] synonym: "cytokine release|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110130 name: biological activity assay measuring epitope specific T cell killing def: "A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110131 name: biological activity assay measuring epitope specific proliferation of T cells def: "A T cell epitope dependent biological activity assay that detects T cell proliferation." [] synonym: "proliferation|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring T cell epitope specific biological activity +is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110132 @@ -24139,171 +25804,191 @@ is_a: OBI:0002062 ! in vitro assay measuring epitope specific T cell killing [Term] id: OBI:1110151 name: ELISA measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|ELISA" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:1110152 name: ELISA measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|ELISA" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:1110153 name: ELISA measuring epitope specific interleukin-4 production by T cells -def: "An assay of epitope specific interleukin-4 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|ELISA" EXACT [] -is_a: OBI:0001450 ! biological activity assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:1110154 name: ELISA measuring epitope specific interleukin-5 production by T cells -def: "An assay of epitope specific interleukin-5 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|ELISA" EXACT [] -is_a: OBI:0001230 ! biological activity assay measuring epitope specific interleukin-5 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:1110155 name: ELISA measuring epitope specific tumor necrosis factor production by T cells -def: "A T cell epitope specific tumor necrosis factor production assay that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects tumor necrosis factor production by T cells." [] synonym: "TNFa release|ELISA" EXACT [] is_a: OBI:0001246 ! ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! biological activity assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells [Term] id: OBI:1110156 name: ELISA measuring epitope specific interleukin-10 production by T cells -def: "An assay of epitope specific interleukin-10 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|ELISA" EXACT [] -is_a: OBI:0001209 ! biological activity assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:1110157 name: ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells -def: "An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|ELISA" EXACT [] -is_a: OBI:0001233 ! biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:1110158 name: ELISA measuring epitope specific interleukin-6 production by T cells -def: "An assay of epitope specific interleukin-6 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|ELISA" EXACT [] -is_a: OBI:0001451 ! biological activity assay measuring epitope specific interleukin-6 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:1110159 name: ELISA measuring epitope specific interleukin-13 production by T cells -def: "An assay of epitope specific interleukin-13 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|ELISA" EXACT [] -is_a: OBI:0001251 ! biological activity assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells [Term] id: OBI:1110160 name: ELISA measuring epitope specific interleukin-12 production by T cells -def: "An assay of epitope specific interleukin-12 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|ELISA" EXACT [] -is_a: OBI:0001391 ! biological activity assay measuring epitope specific interleukin-12 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells [Term] id: OBI:1110161 name: ELISA measuring epitope specific interleukin-1 beta production by T cells -def: "An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|ELISA" EXACT [] -is_a: OBI:0001449 ! biological activity assay measuring epitope specific interleukin-1 beta production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells [Term] id: OBI:1110162 name: ELISA measuring epitope specific interleukin-17 production by T cells -def: "An assay of epitope specific interleukin-17 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|ELISA" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:1110163 name: ELISA measuring epitope specific interleukin-18 production by T cells -def: "An assay of epitope specific interleukin-18 production by T cells that uses an ELISA." [] +def: "An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|ELISA" EXACT [] -is_a: OBI:0001380 ! biological activity assay measuring epitope specific interleukin-18 production by T cells +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells [Term] id: OBI:1110167 name: ELISPOT assay measuring epitope specific interleukin-4 production by T cells -def: "An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|ELISPOT" EXACT [] -is_a: OBI:0001450 ! biological activity assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110168 name: ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells -def: "A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects tumor necrosis factor production by T cells." [] synonym: "TNFa release|ELISPOT" EXACT [] is_a: OBI:0001272 ! ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! biological activity assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells [Term] id: OBI:1110170 name: ELISPOT assay measuring epitope specific interleukin-10 production by T cells -def: "An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|ELISPOT" EXACT [] -is_a: OBI:0001209 ! biological activity assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110171 name: ELISPOT assay measuring epitope specific interleukin-13 production by T cells -def: "An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay." [] +def: "An enzyme-linked immunospot assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|ELISPOT" EXACT [] -is_a: OBI:0001251 ! biological activity assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells +is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110172 name: intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells -def: "An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|ICS" EXACT [] -is_a: OBI:0001414 ! biological activity assay measuring epitope specific interferon-gamma production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:1110173 name: intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells -def: "An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|ICS" EXACT [] -is_a: OBI:0001445 ! biological activity assay measuring epitope specific interleukin-2 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:1110174 name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells -def: "A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects tumor necrosis factor production by T cells." [] synonym: "TNFa release|ICS" EXACT [] is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! biological activity assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells [Term] id: OBI:1110175 name: intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells -def: "An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|ICS" EXACT [] -is_a: OBI:0001450 ! biological activity assay measuring epitope specific interleukin-4 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:1110177 name: intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells -def: "An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|ICS" EXACT [] -is_a: OBI:0001209 ! biological activity assay measuring epitope specific interleukin-10 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:1110178 name: intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells -def: "An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay." [] +def: "A flow cytometry assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|ICS" EXACT [] -is_a: OBI:0001295 ! biological activity assay measuring epitope specific interleukin-17 production by T cells +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:1110179 name: MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex -def: "A T cell epitope qualitative binding assay that uses an MHC multimer staining assay." [] +def: "A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor." [] synonym: "qualitative binding|multimer/tetramer" EXACT [] is_a: OBI:0001317 ! flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex is_a: OBI:0001501 ! fluorescence detection assay @@ -25812,7 +27497,7 @@ is_a: OBI:2100045 ! tobramycin assay id: OBI:2100207 name: CBC with manual differential venous blood myelocyte count assay def: "A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order" [] -is_a: OBI:0003016 ! myelocyte assay +is_a: OBI:0003165 ! myelocyte count assay [Term] id: OBI:2100208 @@ -27574,6 +29259,12 @@ name: double-stranded RNA-specific adenosine deaminase def: "A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000003777 +name: adiponectin +def: "A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000003918 name: albumin @@ -27628,6 +29319,12 @@ name: haptoglobin def: "A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000009758 +name: leptin +def: "A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000013429 name: parathyroid hormone @@ -28727,7 +30424,7 @@ range: IAO:0000027 ! data item [Typedef] id: OBI:0000293 name: has_specified_input -def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +def: "The inverse property of is_specified_input_of" [] domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000295 ! is_specified_input_of @@ -28763,7 +30460,7 @@ is_obsolete: true [Typedef] id: OBI:0000299 name: has_specified_output -def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +def: "The inverse property of is_specified_output_of" [] domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000312 ! is_specified_output_of diff --git a/views/obi_core.owl b/views/obi_core.owl index cd8dd913..28d116fd 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +78,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2021-08-18 + 2022-01-03 @@ -166,9 +166,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -195,9 +195,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -367,9 +367,9 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 IEDB alternative term - An alternative term used by the IEDB. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB + An alternative term used by the IEDB. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB IEDB alternative term @@ -560,12 +560,12 @@ every c that is a concretization of g specifically denotes r is_supported_by_data - The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. + The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process + The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI - Philly 2011 workshop + Philly 2011 workshop is_supported_by_data @@ -582,16 +582,16 @@ every c that is a concretization of g specifically denotes r + has_specified_input has_specified_input - has_specified_input see is_input_of example_of_usage - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + The inverse property of is_specified_input_of + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot has_specified_input @@ -603,12 +603,12 @@ every c that is a concretization of g specifically denotes r - is_specified_input_of + is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_input_of @@ -625,14 +625,14 @@ every c that is a concretization of g specifically denotes r + has_specified_output has_specified_output - has_specified_output - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + The inverse property of is_specified_output_of PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot has_specified_output @@ -649,12 +649,12 @@ every c that is a concretization of g specifically denotes r + is_specified_output_of is_specified_output_of - is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_output_of @@ -667,14 +667,14 @@ every c that is a concretization of g specifically denotes r - achieves_planned_objective - A cell sorting process achieves the objective specification 'material separation objective' + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. - BP, AR, PPPB branch - PPPB branch derived - modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - achieves_planned_objective + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + achieves_planned_objective @@ -684,12 +684,12 @@ every c that is a concretization of g specifically denotes r - objective_achieved_by + objective_achieved_by - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - objective_achieved_by + objective_achieved_by @@ -872,7 +872,7 @@ every c that is a concretization of g specifically denotes r - derives from + derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) @@ -1660,11 +1660,11 @@ every c that is a concretization of g specifically denotes r - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - molecular entity + molecular entity @@ -1679,18 +1679,18 @@ every c that is a concretization of g specifically denotes r + cell line cell cell line cell - cell line cell 细胞系细胞 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 - 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 + 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 + cell line cell cell line cell - cell line cell 细胞系细胞 @@ -1711,13 +1711,13 @@ every c that is a concretization of g specifically denotes r + cell cell - cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + cell cell - cell @@ -1726,10 +1726,10 @@ every c that is a concretization of g specifically denotes r - primary cultured cell - A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. + primary cultured cell + A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. - primary cultured cell + primary cultured cell @@ -1738,10 +1738,10 @@ every c that is a concretization of g specifically denotes r - cultured cell - A cell in vitro that is or has been maintained or propagated as part of a cell culture. + cultured cell + A cell in vitro that is or has been maintained or propagated as part of a cell culture. - cultured cell + cultured cell @@ -1757,10 +1757,10 @@ every c that is a concretization of g specifically denotes r - experimentally modified cell in vitro - A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. + experimentally modified cell in vitro + A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. - experimentally modified cell in vitro + experimentally modified cell in vitro @@ -1769,10 +1769,10 @@ every c that is a concretization of g specifically denotes r - environmental material - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. + environmental material + A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. - environmental material + environmental material @@ -1789,10 +1789,10 @@ every c that is a concretization of g specifically denotes r - molecular_function - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular_function + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. - molecular_function + molecular_function @@ -1801,10 +1801,10 @@ every c that is a concretization of g specifically denotes r - cellular_component - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + cellular_component + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - cellular_component + cellular_component @@ -1814,10 +1814,10 @@ every c that is a concretization of g specifically denotes r - biological_process - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological_process + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - biological_process + biological_process @@ -2367,9 +2367,9 @@ Request that IAO either clarify these or change definitions not to use them - Viruses + Viruses - Viruses + Viruses @@ -2378,10 +2378,10 @@ Request that IAO either clarify these or change definitions not to use them - Euteleostomi - bony vertebrates + Euteleostomi + bony vertebrates - Euteleostomi + Euteleostomi @@ -2390,10 +2390,10 @@ Request that IAO either clarify these or change definitions not to use them - Bacteria - eubacteria + Bacteria + eubacteria - Bacteria + Bacteria @@ -2402,9 +2402,9 @@ Request that IAO either clarify these or change definitions not to use them - Archaea + Archaea - Archaea + Archaea @@ -2413,11 +2413,11 @@ Request that IAO either clarify these or change definitions not to use them - Eukaryota - eucaryotes - eukaryotes + Eukaryota + eucaryotes + eukaryotes - Eukaryota + Eukaryota @@ -2426,9 +2426,9 @@ Request that IAO either clarify these or change definitions not to use them - Euarchontoglires + Euarchontoglires - Euarchontoglires + Euarchontoglires @@ -2437,10 +2437,10 @@ Request that IAO either clarify these or change definitions not to use them - Tetrapoda - tetrapods + Tetrapoda + tetrapods - Tetrapoda + Tetrapoda @@ -2449,10 +2449,10 @@ Request that IAO either clarify these or change definitions not to use them - Amniota - amniotes + Amniota + amniotes - Amniota + Amniota @@ -2461,9 +2461,9 @@ Request that IAO either clarify these or change definitions not to use them - Opisthokonta + Opisthokonta - Opisthokonta + Opisthokonta @@ -2472,9 +2472,9 @@ Request that IAO either clarify these or change definitions not to use them - Bilateria + Bilateria - Bilateria + Bilateria @@ -2483,10 +2483,10 @@ Request that IAO either clarify these or change definitions not to use them - Mammalia - mammals + Mammalia + mammals - Mammalia + Mammalia @@ -2495,11 +2495,11 @@ Request that IAO either clarify these or change definitions not to use them - Vertebrata <vertebrates> - Vertebrata - vertebrates + Vertebrata <vertebrates> + Vertebrata + vertebrates - Vertebrata <vertebrates> + Vertebrata <vertebrates> @@ -2508,12 +2508,12 @@ Request that IAO either clarify these or change definitions not to use them - Homo sapiens - human - human being - man + Homo sapiens + human + human being + man - Homo sapiens + Homo sapiens @@ -2533,17 +2533,17 @@ Request that IAO either clarify these or change definitions not to use them + planned process planned process - planned process - Injecting mice with a vaccine in order to test its efficacy + Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process @@ -2615,16 +2615,16 @@ objectives is a planned process. investigation - Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation + Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived - Could add specific objective specification + Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS - study + study investigation @@ -2652,9 +2652,9 @@ editor = PRS a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") - GROUP: Role Branch - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role @@ -2722,7 +2722,7 @@ editor = PRS assay - Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. @@ -2730,8 +2730,8 @@ editor = PRS measuring scientific observation OBI branch derived - study assay - any method + study assay + any method assay @@ -2741,14 +2741,14 @@ editor = PRS - reagent role + reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush - reagent - PERSON:Matthew Brush - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + reagent + PERSON:Matthew Brush + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. @@ -2786,15 +2786,15 @@ In regard to the statement that reagents are 'distinct' from the speci - material processing - A cell lysis, production of a cloning vector, creating a buffer. + material processing + A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca Serra + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing @@ -2813,14 +2813,14 @@ In regard to the statement that reagents are 'distinct' from the speci study subject role - Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. + Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. - A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. + A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch - OBI + OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. @@ -2854,20 +2854,20 @@ editor = PRS - specimen role - liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation - 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. - GROUP: Role Branch - OBI + GROUP: Role Branch + OBI specimen role @@ -2932,19 +2932,19 @@ http://code.google.com/p/popcomm-ontology/ - investigation agent role + investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. - Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. + Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch - investigator + investigator OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - study person role + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) - investigation agent role + investigation agent role @@ -2984,11 +2984,11 @@ This leads to my proposal: We define organization through the statements 1 - current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - PERSON: Susanna Sansone - GROUP: OBI + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI organization @@ -3004,7 +3004,7 @@ for now. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) - study protocol + study protocol protocol @@ -3026,13 +3026,13 @@ for now. - interpreting data - Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. + interpreting data + Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - Bjoern Peters + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + Bjoern Peters drawing a conclusion based on data @@ -3053,14 +3053,14 @@ for now. - planning - The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. + planning + The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification - 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. - Bjoern Peters - Bjoern Peters - Plans and Planned Processes Branch + 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. + Bjoern Peters + Bjoern Peters + Plans and Planned Processes Branch planning @@ -3070,12 +3070,12 @@ for now. - analyte measurement objective - The objective to measure the concentration of glucose in a blood sample + analyte measurement objective + The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant - PERSON: Bjoern Peters - PPPB branch + PERSON: Bjoern Peters + PPPB branch analyte measurement objective @@ -3085,12 +3085,12 @@ for now. - assay objective - the objective to determine the weight of a mouse. + assay objective + the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) - PPPB branch - PPPB branch + PPPB branch + PPPB branch assay objective @@ -3113,18 +3113,18 @@ for now. analyte assay - example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output + example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output - An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. - Alan Ruttenberg - Bjoern Peters - Helen Parkinson - Philippe Rocca-Serra - Alan Ruttenberg - Bjoern Peters - Helen Parkinson - OBI Planned process branch - Philippe Rocca-Serra + An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. + Alan Ruttenberg + Bjoern Peters + Helen Parkinson + Philippe Rocca-Serra + Alan Ruttenberg + Bjoern Peters + Helen Parkinson + OBI Planned process branch + Philippe Rocca-Serra analyte assay @@ -3152,13 +3152,13 @@ for now. measure function - A glucometer measures blood glucose concentration, the glucometer has a measure function. + A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. - PERSON: Daniel Schober - PERSON: Helen Parkinson - PERSON: Melanie Courtot - PERSON:Frank Gibson + PERSON: Daniel Schober + PERSON: Helen Parkinson + PERSON: Melanie Courtot + PERSON:Frank Gibson measure function @@ -3168,17 +3168,17 @@ for now. - material transformation objective - The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra artifact creation objective - GROUP: OBI PlanAndPlannedProcess Branch + GROUP: OBI PlanAndPlannedProcess Branch material transformation objective @@ -3204,15 +3204,15 @@ for now. - study design execution - injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. + study design execution + injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. - a planned process that carries out a study design - removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. - branch derived - 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. + a planned process that carries out a study design + removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. + branch derived + 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution + study design execution @@ -3247,16 +3247,16 @@ for now. specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation - A planned process with the objective of collecting a specimen. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ - Bjoern Peters + Bjoern Peters specimen collection - 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession - 6/9/09: used at workshop + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop specimen collection process @@ -3267,11 +3267,11 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection objective - The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - A objective specification to obtain a material entity for potential use as an input during an investigation. - Bjoern Peters - Bjoern Peters + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters specimen collection objective @@ -3287,20 +3287,20 @@ http://sourceforge.net/p/obi/obi-terms/716/ - independent variable specification + independent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert experimental factor independent variable - Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. - study factor + Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + study factor study design independent variable @@ -3316,18 +3316,18 @@ http://sourceforge.net/p/obi/obi-terms/716/ - dependent variable specification + dependent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert dependent variable - WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design dependent variable @@ -3343,18 +3343,18 @@ http://sourceforge.net/p/obi/obi-terms/716/ - controlled variable specification + controlled variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert controlled variable - WEB: http://en.wikipedia.org/wiki/Control_variable - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + WEB: http://en.wikipedia.org/wiki/Control_variable + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design controlled variable @@ -3381,14 +3381,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - informed consent process + informed consent process - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. - 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#informed - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informed consent process + A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#informed + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informed consent process @@ -3408,13 +3408,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - measurement device - A ruler, a microarray scanner, a Geiger counter. + measurement device + A ruler, a microarray scanner, a Geiger counter. - A device in which a measure function inheres. - GROUP:OBI Philly workshop - OBI - measurement device + A device in which a measure function inheres. + GROUP:OBI Philly workshop + OBI + measurement device @@ -3432,15 +3432,15 @@ http://sourceforge.net/p/obi/obi-terms/716/ - processed specimen + processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. - A specimen that has been intentionally physically modified. - Bjoern Peters - Bjoern Peters + A specimen that has been intentionally physically modified. + Bjoern Peters + Bjoern Peters A tissue sample that has been sliced and stained for a histology study. - processed specimen + processed specimen @@ -3472,12 +3472,12 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: @@ -3488,10 +3488,10 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device @@ -3522,14 +3522,14 @@ In the examples above, a reagent is an operational component of a device, but th - secondary cultured cell + secondary cultured cell - A cultured cell that has been passaged or derives from a cell that has been passaged in culture. - The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + A cultured cell that has been passaged or derives from a cell that has been passaged in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush - PERSON: Matthew Brush - A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. - secondary cultured cell + PERSON: Matthew Brush + A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. + secondary cultured cell @@ -3706,11 +3706,11 @@ The following are NOT conclusions based on data: data themselves; results from p cytometry assay - An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. + An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. - An assay that counts and/or measures characteristics of cells. - IEDB - IEDB + An assay that counts and/or measures characteristics of cells. + IEDB + IEDB cytometry assay @@ -3765,11 +3765,11 @@ The following are NOT conclusions based on data: data themselves; results from p virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism @@ -3792,12 +3792,12 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - PERSON: James Malone - PERSON: Philippe Rocca-Serra + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen @@ -3843,14 +3843,14 @@ This issue is outside the scope of OBI. data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard @@ -3892,9 +3892,9 @@ This issue is outside the scope of OBI. study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. - PERSON: Chris Stoeckert + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. @@ -3986,7 +3986,7 @@ defines and states the requirements (positive or negative) for an entity to be c enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. - As with group assignment, should the specified output here be an organism which bears a role + As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch @@ -4024,10 +4024,10 @@ defines and states the requirements (positive or negative) for an entity to be c acquisition - Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. + Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. the planned process of gaining possession of a continuant - 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. + 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule' @@ -4053,10 +4053,10 @@ Relates to the creation of a class 'selection rule' Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. An acquisition in which possession of a material entity is gained. - The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation + The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation This excludes processes that create or change materials, such as material transformations. Bjoern Peters, Alan Ruttenberg, Helen Parkinson - material procurement + material procurement IEDB material acquisition @@ -4079,7 +4079,7 @@ Relates to the creation of a class 'selection rule' An acquisition in which possession of information is gained. This excludes processes that create or change information, such as assays and data transformations. Bjoern Peters - data collection + data collection OBI branch derived information acquisition @@ -4110,7 +4110,7 @@ Relates to the creation of a class 'selection rule' disease course The totality of all processes through which a given disease instance is realized. - replace 'OBI:occurrence of disease', need to add logical definition + replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease @@ -4186,7 +4186,7 @@ realizes some 'host of immune response role' organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release - PERSON:Alan Ruttenberg + PERSON:Alan Ruttenberg organizational term @@ -4358,8 +4358,8 @@ realizes some 'host of immune response role' --> - A reference to a place on the Earth, by its name or by its geographical location. - geographic location + A reference to a place on the Earth, by its name or by its geographical location. + geographic location