From 02ddc889bcd043bdb4d313de8da1d4af7025f616 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 27 Jun 2024 10:47:49 -0500 Subject: [PATCH 1/3] Add lang tags to obi-edit and templates --- src/ontology/obi-edit.owl | 1362 ++++++++--------- src/ontology/templates/administration.tsv | 2 +- .../templates/antibody-purification.tsv | 2 +- src/ontology/templates/assays.tsv | 2 +- src/ontology/templates/biobank-specimens.tsv | 4 +- src/ontology/templates/biopsy.tsv | 2 +- src/ontology/templates/data-sets.tsv | 2 +- .../templates/data-transformations.tsv | 2 +- src/ontology/templates/devices.tsv | 2 +- src/ontology/templates/epitope-assays.tsv | 2 +- src/ontology/templates/medical-history.tsv | 2 +- src/ontology/templates/obsolete.tsv | 2 +- src/ontology/templates/organizations.tsv | 2 +- .../templates/physical-examination.tsv | 2 +- src/ontology/templates/sample-collection.tsv | 2 +- src/ontology/templates/sequence-analysis.tsv | 2 +- .../templates/specimen-assay-data.tsv | 2 +- src/ontology/templates/study-designs.tsv | 2 +- .../templates/value-specifications.tsv | 2 +- 19 files changed, 700 insertions(+), 700 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 037b4160..e9c418e5 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -301,7 +301,7 @@ - An alternative term used by the ISA tools project (http://isa-tools.org). + An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran @@ -317,7 +317,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). + An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term @@ -330,7 +330,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An alternative term used by the IEDB. + An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term @@ -343,7 +343,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An alternative term used by the Functional Genomics Data (FGED) Society. + An alternative term used by the Functional Genomics Data (FGED) Society. PERSON: Chris Stoeckert, Jie Zheng Penn Group FGED alternative term @@ -651,7 +651,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. - A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. + A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with @@ -664,7 +664,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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 @@ -698,7 +698,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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. + 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 @@ -730,7 +730,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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. + 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 @@ -747,7 +747,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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 @@ -784,7 +784,7 @@ 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] + 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 @@ -837,7 +837,7 @@ 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 - Relation between an independent continuant and a function. + 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 @@ -874,7 +874,7 @@ 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 @@ -997,7 +997,7 @@ level of radioactivity is_proxy_for level of toxicity has_role - A relation between a continuant C and a role R. The reciprocal relation of role_of. + 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 @@ -1030,7 +1030,7 @@ 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. + 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 @@ -1044,7 +1044,7 @@ level of radioactivity is_proxy_for level of toxicity 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. + 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 @@ -1060,7 +1060,7 @@ level of radioactivity is_proxy_for level of toxicity 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 @@ -1074,7 +1074,7 @@ level of radioactivity is_proxy_for level of toxicity obsoleted_is_specified_information_intput_of - Is the inverse relation of has_specfied_input_information + Is the inverse relation of has_specfied_input_information is replaced by is_specified_intput_of obsoleted_is_specified_information_intput_of @@ -1088,7 +1088,7 @@ level of radioactivity is_proxy_for level of toxicity 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. + 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. PERSON: Alan Ruttenberg Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 @@ -1102,7 +1102,7 @@ level of radioactivity is_proxy_for level of toxicity 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 supplies @@ -1125,7 +1125,7 @@ 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. + 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 @@ -1142,7 +1142,7 @@ level of radioactivity is_proxy_for level of toxicity 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 @@ -1164,7 +1164,7 @@ 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. + 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 @@ -1184,7 +1184,7 @@ level of radioactivity is_proxy_for level of toxicity 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. + 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 @@ -1197,7 +1197,7 @@ level of radioactivity is_proxy_for level of toxicity has disposition to bind - A relationship between two material entitites that each have disposition to form a complex with the other. + 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 @@ -1217,7 +1217,7 @@ level of radioactivity is_proxy_for level of toxicity - Relating an organization to a legal person or organization. + 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 @@ -1231,7 +1231,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a value specification and an entity which the specification is about. + A relation between a value specification and an entity which the specification is about. specifies value of @@ -1244,7 +1244,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between an information content entity and a value specification that specifies its value. + A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification @@ -1275,7 +1275,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. + A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI OBI The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). @@ -1288,7 +1288,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. + A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1516 @@ -1305,7 +1305,7 @@ 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 - is a relationship between a process and a preceding occurrent that directly caused the later one to occur + 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 @@ -1331,7 +1331,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ bound_to - A relationship between two material entities that form a complex based on a selective, non-covalent interaction. + 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 @@ -1481,7 +1481,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a value specification and a number that quantifies it. + A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI @@ -1494,7 +1494,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a value specification and a literal. + A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value @@ -3160,7 +3160,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ 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 OBI, CDISC @@ -3371,7 +3371,7 @@ 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 - A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization + 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 @@ -3441,7 +3441,7 @@ 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 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. + 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 @@ -3630,7 +3630,7 @@ objectives is a planned process. 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 role @@ -3917,7 +3917,7 @@ editor = PRS 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. + 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 @@ -3988,7 +3988,7 @@ In regard to the statement that reagents are 'distinct' from the speci detector reagent role - a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. + 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 @@ -4003,7 +4003,7 @@ In regard to the statement that reagents are 'distinct' from the speci 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 + 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 @@ -4103,7 +4103,7 @@ In regard to the statement that reagents are 'distinct' from the speci 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 @@ -4193,7 +4193,7 @@ editor = PRS 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 @@ -4331,7 +4331,7 @@ 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 @@ -4371,7 +4371,7 @@ specimen can later be subject. 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 role @@ -4462,7 +4462,7 @@ specimen can later be subject. 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 - the role of a organization that is realized by members reviewing study designs for their agreement with regulations + 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 @@ -4493,7 +4493,7 @@ specimen can later be subject. 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 role @@ -4508,7 +4508,7 @@ specimen can later be subject. 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 role @@ -4584,7 +4584,7 @@ addition of has_role restriction 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 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. @@ -4708,7 +4708,7 @@ http://code.google.com/p/popcomm-ontology/ 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: Jennifer Fostel @@ -4739,7 +4739,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 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 OBI @@ -4898,7 +4898,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 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 role @@ -4914,7 +4914,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 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 @@ -4988,7 +4988,7 @@ An individual or juridicial or other body authorized under applicable law to con vital dye role typtan blue has a vital dye - A dye role that is realized when used to detect live cells in an experiment + 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 @@ -5237,7 +5237,7 @@ for now. 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 OBI @@ -5253,7 +5253,7 @@ for now. 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 role @@ -5267,7 +5267,7 @@ 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 @@ -5895,7 +5895,7 @@ Proposal is to obsolete. 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. + 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 @@ -5941,7 +5941,7 @@ 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. + 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 @@ -6279,7 +6279,7 @@ Proposal is to obsolete. 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. + 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 @@ -6325,7 +6325,7 @@ 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 - The extraction of RNA from an input material that specifically isolates viral RNA + The extraction of RNA from an input material that specifically isolates viral RNA Person:Bjoern Peters viral RNA extraction @@ -6351,7 +6351,7 @@ Proposal is to obsolete. 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 @@ -6373,7 +6373,7 @@ Proposal is to obsolete. recombinant plasmid - a plasmid in which extraneous DNA has been inserted. + a plasmid in which extraneous DNA has been inserted. PERSON: Bjoern Peters PERSON: Kevin Clancy PERSON: Melanie Courtot @@ -6759,7 +6759,7 @@ 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 - A process in which an input substance is injected into a organ section. + A process in which an input substance is injected into a organ section. Person:Bjoern Peters injection into organ section @@ -6878,7 +6878,7 @@ 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. - A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. + A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. 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 @@ -7086,7 +7086,7 @@ 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. - a planned process that carries out 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. @@ -7120,7 +7120,7 @@ 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. - a process in which a population of cells with certain characteristics is isolated from a larger 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 @@ -7145,7 +7145,7 @@ that has_part some material entity is a material entity. If we add as equivalent 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. + 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 @@ -7176,7 +7176,7 @@ 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. - a process in which cells with a single nucleus are isolated from a blood sample + 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 @@ -7222,7 +7222,7 @@ that has_part some material entity is a material entity. If we add as equivalent 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. + 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 @@ -7258,7 +7258,7 @@ 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 is a role which inheres in a person or organization and which is realized by a manufacturing process. + 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 @@ -7309,7 +7309,7 @@ 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. - is an objective to transform a material entity into spatially separated components. + is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective @@ -7407,7 +7407,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 urine specimen - a portion of urine collected from an organism + 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? @@ -7441,7 +7441,7 @@ 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. - is a material processing with the objective to combine two or more material entities as input into a single material entity as output. + 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 @@ -7478,7 +7478,7 @@ 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 - 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 @@ -7511,7 +7511,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 blood specimen blood drawn from a human for glucose assay - a material entity derived from a portion of blood collected from an organism + a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen @@ -7548,7 +7548,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 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. + 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 @@ -7587,7 +7587,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 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. + 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. @@ -7746,7 +7746,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ sample from organism - a material obtained from an organism in order to be a representative of the whole + 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 @@ -7801,7 +7801,7 @@ 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 @@ -7839,7 +7839,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective @@ -7896,7 +7896,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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 + 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 @@ -7910,7 +7910,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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). + 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 @@ -7923,7 +7923,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective @@ -7962,7 +7962,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -7976,7 +7976,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ material combination objective - is an objective to obtain an output material that contains several input materials. + is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective @@ -7991,7 +7991,7 @@ 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 is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation + 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 @@ -8005,7 +8005,7 @@ 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. - A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. + 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 @@ -8032,7 +8032,7 @@ 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. - is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity + 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 @@ -8046,7 +8046,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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 + 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 @@ -8077,7 +8077,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ animal feeding giving crickets to a snake. - animal feeding is a process in which animals are provided with food + 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 @@ -8098,7 +8098,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -8135,7 +8135,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -8151,7 +8151,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -8211,7 +8211,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ laboratory animal care - a process that realizes an animal care protocol that specifies how animals are kept and maintained + a process that realizes an animal care protocol that specifies how animals are kept and maintained laboratory animal care @@ -8229,7 +8229,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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 + 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 @@ -8279,7 +8279,7 @@ 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. - 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. + 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 @@ -8351,7 +8351,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ pathogen challenge - The administration of a live pathogenic organism to a host. + The administration of a live pathogenic organism to a host. pathogen challenge @@ -8363,7 +8363,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ GenePattern software - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + 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/ @@ -8379,7 +8379,7 @@ 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. - 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. + 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 @@ -8396,7 +8396,7 @@ 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. - An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes + 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 @@ -8423,7 +8423,7 @@ 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 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 + 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 @@ -8445,7 +8445,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ vaccine preparation The production of B. pertussis vaccine. - A planned process with the objective to create a vaccine. + A planned process with the objective to create a vaccine. OBI vaccine production @@ -8465,7 +8465,7 @@ 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 - The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. + 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 @@ -8484,7 +8484,7 @@ 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. - is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs + 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 @@ -8507,7 +8507,7 @@ 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 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 + 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 @@ -8524,7 +8524,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -8620,7 +8620,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8644,7 +8644,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8668,7 +8668,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8687,7 +8687,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -8713,7 +8713,7 @@ the role 'adjuvant role' inheres in some 'material entity' a NTP-2000 - a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents + a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents Jennifer Fostel, Bjoern Peters NTP-2000 @@ -8726,7 +8726,7 @@ the role 'adjuvant role' inheres in some 'material entity' a single fragment library - is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs + 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 @@ -8756,7 +8756,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8806,7 +8806,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8831,7 +8831,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8846,7 +8846,7 @@ 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. - A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. + 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 @@ -8861,7 +8861,7 @@ 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. - 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. + 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 @@ -8899,7 +8899,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -8926,7 +8926,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 @@ -8952,7 +8952,7 @@ 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. - A material entity that has the material sample role + A material entity that has the material sample role OBI: workshop sample population @@ -9090,7 +9090,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -9102,7 +9102,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -9117,7 +9117,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9131,7 +9131,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9152,7 +9152,7 @@ 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 - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + 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 @@ -9187,7 +9187,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9203,7 +9203,7 @@ 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. - 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 + 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 @@ -9219,7 +9219,7 @@ http://en.wikipedia.org/wiki/Survival_rate capsule shell - a small rounded gelatinous container + 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 @@ -9235,7 +9235,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9262,7 +9262,7 @@ 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 - A process in which bonds are created that link one polymer to another + 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 @@ -9277,7 +9277,7 @@ 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 - A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. + 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 @@ -9313,7 +9313,7 @@ http://en.wikipedia.org/wiki/Survival_rate denaturing Denaturing DNA in alcohol - Is a process in which the tertiary or secondary structure of a polymer is disrupted + Is a process in which the tertiary or secondary structure of a polymer is disrupted http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denaturing @@ -9356,7 +9356,7 @@ http://en.wikipedia.org/wiki/Survival_rate informing investigator of subject study arm Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound. - A planned process with the objective to make the investigator aware of which study arm a patient is participating in. + A planned process with the objective to make the investigator aware of which study arm a patient is participating in. 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 @@ -9371,7 +9371,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance objective - An objective specification maintains some or all of the qualities of a material over time. + An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective @@ -9402,7 +9402,7 @@ http://en.wikipedia.org/wiki/Survival_rate presentation of stimulus The presentation of a flashing light to a monkey during reward training - A planned process with the objective to expose an organism to a stimulus. + A planned process with the objective to expose an organism to a stimulus. Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom @@ -9429,7 +9429,7 @@ http://en.wikipedia.org/wiki/Survival_rate amplified DNA Amplied DNA created by PCR - DNA that has been produced in an enzymatic amplification process + DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA @@ -9460,7 +9460,7 @@ http://en.wikipedia.org/wiki/Survival_rate informed consent process - A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. + A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in 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 @@ -9487,7 +9487,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9502,7 +9502,7 @@ 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 - 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 + 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 @@ -9517,7 +9517,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9531,7 +9531,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9546,7 +9546,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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). + 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 @@ -9573,7 +9573,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9611,7 +9611,7 @@ http://en.wikipedia.org/wiki/Survival_rate anticoagulant tube storage of blood specimen - Storage of a blood specimen in a tube with anticoagulant + 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 @@ -9631,7 +9631,7 @@ http://en.wikipedia.org/wiki/Survival_rate filled capsule - A pill in the form of a small rounded gelatinous container with medicine inside. + 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 @@ -9660,7 +9660,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9676,7 +9676,7 @@ 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 is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material + 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 @@ -9690,7 +9690,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9710,7 +9710,7 @@ http://en.wikipedia.org/wiki/Survival_rate treatment portion of study execution - A planned process, part of a study design execution, during which the treatment of subjects is ongoing + 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 @@ -9725,7 +9725,7 @@ http://en.wikipedia.org/wiki/Survival_rate pill - A dose of medicine or placebo in the form of a small pellet. + 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 @@ -9741,7 +9741,7 @@ http://en.wikipedia.org/wiki/Survival_rate research organization The SALK institute is a research organization. - An organization formed with a goal to have its members conduct investigations + An organization formed with a goal to have its members conduct investigations Person:Bjoern Peters research organization @@ -9754,7 +9754,7 @@ http://en.wikipedia.org/wiki/Survival_rate DNA residue methylation - a quality of a DNA residue that has a methyl group attached to it + a quality of a DNA residue that has a methyl group attached to it DNA residue methylation @@ -9767,7 +9767,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9797,7 +9797,7 @@ http://en.wikipedia.org/wiki/Survival_rate manufacturer - A person or organization that has a manufacturer role. + A person or organization that has a manufacturer role. manufacturer @@ -9815,7 +9815,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance - A planned process with the objective to maintain some or all of the characteristics of an input material over time. + A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance @@ -9840,7 +9840,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9869,7 +9869,7 @@ placeholder unblinding process - A planned process that is 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. + A planned process that is 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 @@ -9889,7 +9889,7 @@ placeholder subject agrees they understand informed consent document - A planned process in which a subject receives an informed consent document and agrees that they have understood it. + A planned 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 @@ -9924,7 +9924,7 @@ placeholder informing subject of study arm Informing participants whether they are receiving a placebo or a treatment with an investigational compound. - A planned process with the objective to make the subject aware of which study arm they are participating in. + A planned process with the objective to make the subject aware of which study arm they are participating in. 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 @@ -9950,7 +9950,7 @@ placeholder 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 + 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 @@ -9964,7 +9964,7 @@ placeholder 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 + 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 @@ -9978,7 +9978,7 @@ placeholder polyA RNA extraction - A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. + 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 @@ -9993,7 +9993,7 @@ placeholder organellar RNA extraction - A RNA extraction process in which the desired output material is RNA in the organelle(s). + A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10009,7 +10009,7 @@ 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. - An information content entity created to indicate that information about something is not available to the person recording it. + An 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 @@ -10024,7 +10024,7 @@ placeholder total RNA extraction - A RNA extraction process in which total cellular and organelle RNA are extracted. + A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10047,7 +10047,7 @@ placeholder 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 + 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 @@ -10067,7 +10067,7 @@ 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. - a record indicating that the biological sex of an organism is not known. + 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 @@ -10081,7 +10081,7 @@ placeholder cytoplasmic RNA extraction - A RNA extraction process in which the desired output material is RNA in the cytoplasm. + A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10096,7 +10096,7 @@ placeholder 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. + 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 @@ -10116,7 +10116,7 @@ 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) - 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. + 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 @@ -10138,7 +10138,7 @@ placeholder 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 + 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 @@ -10152,7 +10152,7 @@ placeholder 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. + 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 @@ -10173,7 +10173,7 @@ 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.) - 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. + 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 @@ -10216,7 +10216,7 @@ placeholder pre-mortem specimen material obtained through a liver biopsy from a human patient - a specimen that was taken from a live organism + a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen @@ -10237,7 +10237,7 @@ 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.) - A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. + 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 @@ -10265,7 +10265,7 @@ placeholder 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 'establishing immortal cell line through directed genetic modification' @@ -10284,7 +10284,7 @@ placeholder 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 + 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 @@ -10313,7 +10313,7 @@ Person: Chris Stoeckert RNA extract - an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. + 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 @@ -10328,7 +10328,7 @@ Person: Chris Stoeckert 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 @@ -10344,7 +10344,7 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La nuclear RNA extraction - A RNA extraction process in which the desired output material is RNA in the nucleus. + A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10395,7 +10395,7 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La 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, + 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 @@ -10416,7 +10416,7 @@ 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. - A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. + 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 @@ -10432,7 +10432,7 @@ 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. - + 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 @@ -10453,7 +10453,7 @@ 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. - 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. + 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 @@ -10495,7 +10495,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. post mortem specimen the spleen taken from a dead mouse - a specimen that was taken from a dead organism + a specimen that was taken from a dead organism Bjoern Peters MO_416 postmortem post mortem specimen @@ -10509,7 +10509,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. sequence feature annotation - Information about a sequence region + Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term @@ -10530,7 +10530,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. induced hemagglutination - The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances + 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 @@ -10555,7 +10555,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t supplying Jackson Labs supplies mouse strains. - A planned process with the objective to provide material entities to be used in an investigation. + A planned process with the objective to provide 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. @@ -10600,7 +10600,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t 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. + 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 @@ -10623,7 +10623,7 @@ Added duirng Mar 1, 2010 dev call 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 @@ -10646,7 +10646,7 @@ stained with fecal material and is then placed in transport medium.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 @@ -10702,7 +10702,7 @@ aspiration. freezing storage a fozen pellet used for later assay - A storage process in temperature that maintenance the frozen status of the stored entities. + 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. @@ -10733,7 +10733,7 @@ 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 - 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 @@ -10762,7 +10762,7 @@ exudate and epithelial debris for microbiological or cellular examination. Dulbecco's modified Eagle medium - A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. + 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 @@ -10785,7 +10785,7 @@ exudate and epithelial debris for microbiological or cellular examination.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 + 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 @@ -10831,7 +10831,7 @@ exudate and epithelial debris for microbiological or cellular examination. 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. + 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 @@ -10881,7 +10881,7 @@ Added duirng Mar 1, 2010 dev call frozen specimen Frozen blood plasma - A specimen that has been frozen in order to store it. + A specimen that has been frozen in order to store it. Person:Alan Ruttenberg MO_610 frozen_sample frozen specimen @@ -10909,7 +10909,7 @@ Added duirng Mar 1, 2010 dev call labeled specimen - A specimen that has been modified in order to be able to detect it in future experiments + 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 @@ -10956,7 +10956,7 @@ Added duirng Mar 1, 2010 dev call lyophilization storage - a storage process with input material entity and output freeze dried material for long time storage + a storage process with input material entity and output freeze dried material for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng @@ -10973,7 +10973,7 @@ Added duirng Mar 1, 2010 dev call 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. + A material separation function is a function that decreases the resolution between two or more material entities. Helen Parkinson OBI material combination function @@ -11022,7 +11022,7 @@ Added duirng Mar 1, 2010 dev call study intervention - A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. + A planned process that is 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 @@ -11042,7 +11042,7 @@ Added duirng Mar 1, 2010 dev call categorical measurement datum - A measurement datum that is reported on a categorical scale. + A measurement datum that is reported on a categorical scale. Bjoern Peters nominal mesurement datum Bjoern Peters @@ -11064,7 +11064,7 @@ 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 - a process that achieves a training objective + a process that achieves a training objective training process @@ -11090,7 +11090,7 @@ Added duirng Mar 1, 2010 dev call 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 + a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role @@ -11134,7 +11134,7 @@ Added duirng Mar 1, 2010 dev call 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 + 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 @@ -11148,7 +11148,7 @@ Biochimie. 2010 Feb 18. sterilization function - a function to remove viable organisms from an input material + a function to remove viable organisms from an input material sterilization function @@ -11180,7 +11180,7 @@ 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. - 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 + 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 @@ -11194,7 +11194,7 @@ 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 - is realized in a planned process where the bearer participates + 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 @@ -11240,7 +11240,7 @@ Biochimie. 2010 Feb 18. paraffin specimen liver tissue embedded in paraffin - a specimen that is output of a paraffin storage process in which specimen is 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 @@ -11264,7 +11264,7 @@ Biochimie. 2010 Feb 18. 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. + 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. @@ -11280,7 +11280,7 @@ 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. - A function that is realized when a reagent is automatically added to some research material. + 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? @@ -11296,7 +11296,7 @@ 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. - A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. + 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 @@ -11311,7 +11311,7 @@ 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 - An objective specification which is fulfilled by the provision of some training. + An objective specification which is fulfilled by the provision of some training. Helen Parkinson OBI training objective @@ -11326,7 +11326,7 @@ 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. - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + 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 @@ -11372,7 +11372,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.lyophilized specimen freezing dried DNA - a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. + 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 @@ -11412,7 +11412,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.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. + 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: @@ -11439,7 +11439,7 @@ 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 - a directive information entity that describes the dose that will be administered to a target + a directive information entity that describes the dose that will be administered to a target dose specification @@ -11482,7 +11482,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11508,7 +11508,7 @@ 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. - 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 sequence data @@ -11542,7 +11542,7 @@ In the examples above, a reagent is an operational component of a device, but th 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 + 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 @@ -11576,7 +11576,7 @@ In the examples above, a reagent is an operational component of a device, but th paraffin storage - a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term 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 @@ -11613,7 +11613,7 @@ In the examples above, a reagent is an operational component of a device, but th agar stab specimen - a specimen that is output of a process that cell culture inoculated into agar for long term storage. + 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 @@ -11629,7 +11629,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11653,7 +11653,7 @@ In the examples above, a reagent is an operational component of a device, but th Edinburgh score - A score that measures the dominance of a person's right or left hand in everyday activities. + 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 @@ -11691,7 +11691,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11705,7 +11705,7 @@ 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 - An objective which is fulfilled by the provision of some service e.g. a training service + An objective which is fulfilled by the provision of some service e.g. a training service Helen Parkinson OBI service provision objective @@ -11736,7 +11736,7 @@ 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. - The directed combination of a material entity with a specimen. + The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen @@ -11750,7 +11750,7 @@ In the examples above, a reagent is an operational component of a device, but th device creation objective - an objective which aims to create a device with a specified function + an objective which aims to create a device with a specified function PERSON: Helen Parkinson OBI device creation objective @@ -11764,7 +11764,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11808,7 +11808,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S agar stab storage - a storage process with input cell culture and agar and output agar stab for long time 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 @@ -11837,7 +11837,7 @@ 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 - A planned process that captures an image of an object. + A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition image creation @@ -11871,7 +11871,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S nucleic acid extract - An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + 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 @@ -11903,7 +11903,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S feature extraction - A planed process with objective of obtaining quantified values from an image. + A planed process with objective of obtaining quantified values from an image. PERSON: Jie Zheng MO_928: feature_extraction @@ -11930,7 +11930,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S array image acquisition - An image creation process that generate an image from the array. + An image creation process that generate an image from the array. PERSON: Jie Zheng array image acquisition MO_929: image_acquisition @@ -11946,7 +11946,7 @@ 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 - a function that allows specific identification of individual speciment from one another. + a function that allows specific identification of individual speciment from one another. EAGLE-I specimen fixation function @@ -11959,7 +11959,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S current amplification function - A current amplification function is an amplification function that increases the amplitude of a current. + A current amplification function is an amplification function that increases the amplitude of a current. EAGLE-I current amplification function @@ -11973,7 +11973,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S 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. + 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 @@ -11987,7 +11987,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S pump function - a transfer unction where the transfer requires work to move the entity, often against a gradient. + a transfer unction where the transfer requires work to move the entity, often against a gradient. EAGLE-I pump function @@ -12001,7 +12001,7 @@ 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. - is a transfer function that displaces cells from one place to another + is a transfer function that displaces cells from one place to another EAGLE-I cell transfer function @@ -12026,7 +12026,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S DNA extract - The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. + 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 @@ -12056,7 +12056,7 @@ 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 @@ -12154,7 +12154,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S 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. + 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 @@ -12371,7 +12371,7 @@ 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. - A measurement datum that describes the structural orientation of a material entity in 3D space. + 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 @@ -12384,7 +12384,7 @@ 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. + 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. @@ -12401,7 +12401,7 @@ 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. + 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 @@ -12415,7 +12415,7 @@ 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. + 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 @@ -12443,7 +12443,7 @@ 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. + 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 @@ -12458,7 +12458,7 @@ 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. + 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 @@ -12472,7 +12472,7 @@ 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. + 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 @@ -12486,7 +12486,7 @@ 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. + 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 @@ -12506,7 +12506,7 @@ 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 + 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 @@ -12530,7 +12530,7 @@ 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. + 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 @@ -12545,7 +12545,7 @@ 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. + 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 @@ -12565,7 +12565,7 @@ All subtype will be defined by textual definition now. half life datum (t 1/2) - The time it takes for 50% of a class of stochastic processes to occur. + The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters @@ -12580,7 +12580,7 @@ All subtype will be defined by textual definition now. 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. + 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 @@ -12618,7 +12618,7 @@ 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. - A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. + 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 @@ -12632,7 +12632,7 @@ All subtype will be defined by textual definition now. 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. + 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 @@ -12650,7 +12650,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12677,7 +12677,7 @@ 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) 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) @@ -12701,7 +12701,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12714,7 +12714,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 negative binding datum - A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. + A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. negative binding datum @@ -12746,7 +12746,7 @@ 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 + 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 @@ -12776,7 +12776,7 @@ 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) 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. + 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) @@ -12798,7 +12798,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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 + 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 @@ -12821,7 +12821,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific cytokine production by T cells - A process of cytokine production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -12846,7 +12846,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific tolerance induction by T cells - A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. + 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 @@ -12871,7 +12871,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12896,7 +12896,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific T cell activation - A process of T cell activation resulting from the recognition of a T cell epitope. + 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 @@ -12921,7 +12921,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12946,7 +12946,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13007,7 +13007,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific T cell tolerance induction - A process of T cell tolerance induction resulting from the recognition of a T cell epitope. + 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 @@ -13032,7 +13032,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13057,7 +13057,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13082,7 +13082,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13107,7 +13107,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13147,7 +13147,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13172,7 +13172,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13243,7 +13243,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13268,7 +13268,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13307,7 +13307,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13332,7 +13332,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13387,7 +13387,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13427,7 +13427,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific RANTES production by T cells - A process of RANTES production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -13467,7 +13467,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13492,7 +13492,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13517,7 +13517,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13542,7 +13542,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13567,7 +13567,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific cytotoxic T cell degranulation - A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. + 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 @@ -13606,7 +13606,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13688,7 +13688,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) 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. + 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 @@ -13713,7 +13713,7 @@ 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 - A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. + 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 @@ -13738,7 +13738,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) 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. + 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 @@ -13763,7 +13763,7 @@ 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 - A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -13808,7 +13808,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13833,7 +13833,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13858,7 +13858,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13885,7 +13885,7 @@ 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 @@ -13910,7 +13910,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13926,7 +13926,7 @@ 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 - An epitope specific immune intervention in which the induced response targets a T cell epitope + 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 @@ -13956,7 +13956,7 @@ 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. + 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 @@ -13970,7 +13970,7 @@ 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. + 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 @@ -13990,7 +13990,7 @@ 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. + 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 @@ -14024,7 +14024,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - 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). + 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 @@ -14046,7 +14046,7 @@ 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 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 @@ -14060,7 +14060,7 @@ 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. + 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 @@ -14102,7 +14102,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html cell collecting - A planned process that collects cells from culture. + A planned process that collects cells from culture. PERSON: Chris Stoeckert, Jie Zheng MO_982 harvest cell collecting @@ -14131,7 +14131,7 @@ 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. - A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. + 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 @@ -14151,7 +14151,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14167,7 +14167,7 @@ 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 - An epitope specific immune intervention in which the induced response targets a B cell 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 @@ -14182,7 +14182,7 @@ 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 enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. + 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 @@ -14196,7 +14196,7 @@ 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. + 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 @@ -14220,7 +14220,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14266,7 +14266,7 @@ 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. - The process in which a ligand binds to an MHC molecule to form a stable 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 @@ -14287,7 +14287,7 @@ 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. + 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 @@ -14308,7 +14308,7 @@ 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 + 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 @@ -14355,7 +14355,7 @@ 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. + 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 @@ -14370,7 +14370,7 @@ 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 @@ -14392,7 +14392,7 @@ 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. - 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. + 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 @@ -14418,7 +14418,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14444,7 +14444,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14470,7 +14470,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14504,7 +14504,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14527,7 +14527,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14543,7 +14543,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14582,7 +14582,7 @@ 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 - A service which has a material entity as specified input and/or specified output. + A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai @@ -14604,7 +14604,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14632,7 +14632,7 @@ 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. - A service that has some information content entity as input and output. + A service that has some information content entity as input and output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai @@ -14649,7 +14649,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14674,7 +14674,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14696,7 +14696,7 @@ 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 - A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) + 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) @@ -14717,7 +14717,7 @@ 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 - A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. + 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 @@ -14799,7 +14799,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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 + 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 @@ -14825,7 +14825,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14841,7 +14841,7 @@ 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. - A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) + 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) @@ -14856,7 +14856,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14873,7 +14873,7 @@ 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. - A scalar measurement datum that represents the number of events occuring over a time interval + A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum @@ -14898,7 +14898,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14920,7 +14920,7 @@ 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. - 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. + 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 @@ -14942,7 +14942,7 @@ 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. - 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. + 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 @@ -14972,7 +14972,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14993,7 +14993,7 @@ 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 - A sequence data item that is about the primary structure of DNA + 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. @@ -15019,7 +15019,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15034,7 +15034,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15064,7 +15064,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15094,7 +15094,7 @@ 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. - A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. + 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 @@ -15109,7 +15109,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N binding A peptide binding to an MHC molecule to form a complex. - The process of material entities forming complexes. + 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 @@ -15131,7 +15131,7 @@ 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 - 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. + 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 @@ -15146,7 +15146,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15176,7 +15176,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N binding off rate measurement datum (koff) - A rate measurement datum of how quickly bound complexes disassociate + A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) @@ -15205,7 +15205,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N binding on rate measurement datum (kon) - A rate measurement datum of how quickly bound complexes form + A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) @@ -15229,7 +15229,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15568,7 +15568,7 @@ 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 - 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 + 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 @@ -15615,7 +15615,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 epitope specific granulysin production by T cells - A process of granulysin production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -15640,7 +15640,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 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. + 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 @@ -15661,7 +15661,7 @@ 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? @@ -15757,7 +15757,7 @@ 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. - a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). + 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 @@ -15771,7 +15771,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 immunoglobulin mediated histamine release - The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. + 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 @@ -15796,7 +15796,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific opsonization - opsonization resulting from antibody binding to epitope + 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 @@ -15821,7 +15821,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific immunoglobulin-mediated neutralization - immunoglobulin-mediated neutralization resulting from antibody binding to epitope + 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 @@ -15846,7 +15846,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific complement-dependent cytotoxicity - complement-dependent cytotoxicity resulting from antibody binding to epitope + 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 @@ -15871,7 +15871,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific antibody-dependent cellular cytotoxicity - antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope + 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 @@ -15893,7 +15893,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific immune complex formation - immune complex formation resulting from antibody binding to epitope + 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 @@ -15918,7 +15918,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific hypersensitivity - hypersensitivity resulting from antibody binding to epitope + 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 @@ -15943,7 +15943,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific histamine secretion mediated by immunoglobulin - histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope + 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 @@ -16018,7 +16018,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - An Investigation agent role borne by a person or organization which + An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group @@ -16043,7 +16043,7 @@ is realized in a specimen collection process. - A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16067,7 +16067,7 @@ is realized in a specimen collection process. - A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16091,7 +16091,7 @@ is realized in a specimen collection process. - A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16115,7 +16115,7 @@ is realized in a specimen collection process. - A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16139,7 +16139,7 @@ is realized in a specimen collection process. - A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16163,7 +16163,7 @@ is realized in a specimen collection process. - A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16191,7 +16191,7 @@ is realized in a specimen collection process. Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. 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. - A planned process in which new information is inferred from existing information. + A planned process in which new information is inferred from existing information. drawing a conclusion @@ -16202,7 +16202,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A transcription profiling identification objective that aims to characterize the transcription start sites of genes. + A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective @@ -16225,7 +16225,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. + A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project @@ -16239,7 +16239,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A sequence feature identification objective that aims to characterize the interactions between protein and RNA. + A sequence feature identification objective that aims to characterize the interactions between protein and RNA. JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. Person: Jie Zheng Jie Zheng @@ -16279,7 +16279,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten secondary cultured cell - A cultured cell that has been passaged or derives from a cell that has been passaged in 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 @@ -16301,7 +16301,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten establishing cell line - a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). + a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush @@ -16328,7 +16328,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. + A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion). @@ -16385,7 +16385,7 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo - A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). + A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran @@ -16465,7 +16465,7 @@ PMID: 23587118. cultured immune cell population - a cultured cell population comprised of a single type of immune system cell + 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 @@ -16500,7 +16500,7 @@ PMID: 23587118. cell culture - A material entity comprised of cultured cells and the media in which they are being propagated or stored. + 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. @@ -16571,7 +16571,7 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. + A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at 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 examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush @@ -16601,7 +16601,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the principal investigator providing the specimens for the investigation + An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution @@ -16626,7 +16626,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center + An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution @@ -16674,7 +16674,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. - A plan specification which specifies the type of material that will be assayed in an investigation. + A plan specification which specifies the type of material that will be assayed in an investigation. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Material @@ -16703,7 +16703,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who is the contact representative of a Bioinformatics Resource Center + A person who is the contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact Name @@ -16736,7 +16736,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. - A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. + A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Scope @@ -16781,7 +16781,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that provides a service to store and distribute specimens + An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository @@ -16806,7 +16806,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the person who is contact representative of a Bioinformatics Resource Center + An email address of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email @@ -16835,7 +16835,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who is the contact representative at the sequencing facility + A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact Name @@ -16864,7 +16864,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who is a principal investigator and provides the specimen + A person who is a principal investigator and provides the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name @@ -16889,7 +16889,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the person collecting the specimen + An email address of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's email @@ -16924,7 +16924,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that provides sequence determination service + An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility @@ -16969,7 +16969,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype - An objective specification which indicates the type of data that will be generated and submitted to a database. + An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives @@ -16994,7 +16994,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the person collecting the specimen + An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution @@ -17019,7 +17019,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the contact representative at the sequencing facility + An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email @@ -17044,7 +17044,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who collects the specimen + A person who collects the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector Name @@ -17072,7 +17072,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of Project Method are Sequence, Array, Mass Spectrometry - A plan specification which indicates the assay type used to obtain data. + A plan specification which indicates the assay type used to obtain data. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Method @@ -17097,7 +17097,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the contact representative at the sequencing facility + An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution @@ -17136,7 +17136,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A textual entity that is about any of the aspects of an investigation worth noting + A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments @@ -17188,7 +17188,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey - A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. + A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Capture @@ -17223,7 +17223,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A specimen identifier which is assigned by a specimen repository + A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID @@ -17258,7 +17258,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A specimen identifier which is assigned by a sequencing facility + A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility @@ -17307,7 +17307,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A sample preparation for assay that preparation of nucleic acids for a sequencing assay + A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method @@ -17332,7 +17332,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the principal investigator providing the specimens for the investigation + An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's email @@ -17357,7 +17357,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. + A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC @@ -17390,7 +17390,7 @@ In regard to the statement that reagents are 'distinct' from the speci secondary cultured cell population - A cultured cell population that is derived through one or more passages in culture. + A cultured cell population that is derived through one or more passages in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells 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 secondary cell culture sample @@ -17413,7 +17413,7 @@ In regard to the statement that reagents are 'distinct' from the speci cancer cell line - An immortal cell line derived from a transformed cell that was part of a malignant tumor. + An immortal cell line derived from a transformed cell that was part of a malignant tumor. cancer cell line @@ -17431,7 +17431,7 @@ In regard to the statement that reagents are 'distinct' from the speci 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 + 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 @@ -17443,7 +17443,7 @@ In regard to the statement that reagents are 'distinct' from the speci that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - An information content entity that expresses an assertion that is intended to be tested. + An information content entity that expresses an assertion that is intended to be tested. In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group hypothesis @@ -17472,7 +17472,7 @@ In regard to the statement that reagents are 'distinct' from the speci The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". - An information content entity that is inferred from data. + An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group @@ -17493,7 +17493,7 @@ The following are NOT conclusions based on data: data themselves; results from p primary cell culture - A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. + 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 @@ -17513,7 +17513,7 @@ The following are NOT conclusions based on data: data themselves; results from p cell line culture - A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently 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. @@ -17528,7 +17528,7 @@ The following are NOT conclusions based on data: data themselves; results from p 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. + 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 @@ -17571,7 +17571,7 @@ See Table 4 - A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. + A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. Chris Stoeckert, Jie Zheng LMA MLPA @@ -17588,7 +17588,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. + A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng Group: Penn Group DNA replication identification objective @@ -17601,7 +17601,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A molecular feature identification objective that aims to determine spatial organization of chromatin. + A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective @@ -17652,7 +17652,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A value specification that specifies the mass of some thing. + A value specification that specifies the mass of some thing. PERSON:Bjoern Peters mass value specification @@ -17664,7 +17664,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A value specification that is specifies one category out of a fixed number of nominal categories + A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification @@ -17688,7 +17688,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A value specification that consists of two parts: a numeral and a unit label + A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification @@ -17745,7 +17745,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A planned process in which predicted values for some thing are compared to measured values for that thing. + A planned process in which predicted values for some thing are compared to measured values for that thing. comparing prediction to measurement @@ -17757,7 +17757,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - An information content entity that specifies a value within a classification scheme or on a quantitative scale. + An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification @@ -17797,7 +17797,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. + an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. PERSON:Bjoern Peters predicted value @@ -17819,7 +17819,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A predicted value where the prediction specifies the mass of some thing. + A predicted value where the prediction specifies the mass of some thing. PERSON:Bjoern Peters predicted mass value @@ -17846,7 +17846,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ 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 + 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 OBI developer call, 3-12-12 molecular-labeled material @@ -17913,7 +17913,7 @@ PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly + the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra weighted median item size @@ -17951,7 +17951,7 @@ PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. + N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html @@ -17965,7 +17965,7 @@ PMID: 23587118. - An organization that provides funding support for projects such as investigations. + An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group @@ -17982,7 +17982,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. + A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. PERSON: Jie Zheng, Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 NIAID GSCID-BRC @@ -18019,7 +18019,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. + A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC @@ -18053,7 +18053,7 @@ PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information + N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html @@ -18110,7 +18110,7 @@ PMID: 23587118. - A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. + A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group annotation provider @@ -18135,7 +18135,7 @@ PMID: 23587118. - A textual entity that is used to denote a sequence assembly. + A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group assembly name @@ -18150,7 +18150,7 @@ PMID: 23587118. - A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. + A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC @@ -18192,7 +18192,7 @@ PMID: 23587118. - A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. + A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. Person: Mathias Brochhausen, Jie Zheng WEB: http://en.wikipedia.org/wiki/Flash_freezing flash freezing @@ -18205,7 +18205,7 @@ PMID: 23587118. - A planned process with the objective to bring some material entity to a temperature below its freezing point. + A planned process with the objective to bring some material entity to a temperature below its freezing point. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing @@ -18219,7 +18219,7 @@ PMID: 23587118. competitive binding reference ligand role The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion. - A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. + A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. Bjoern Peters, Randi Vita, James A. Overton Bjoern Peters competitive binding reference ligand role @@ -18308,7 +18308,7 @@ PMID: 23587118. decision-theoretic analysis objective - An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. + An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. The best action to take is typically defined as the one that maximizes expected utility. PERSON: Bill Hogan decision analysis objective @@ -18445,7 +18445,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. + A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ Person:Chris Stoeckert PMID:15905473 @@ -18481,7 +18481,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.enzyme-linked antibody Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL). - A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. + A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. Bjoern Peters, Randi Vita, James A. Overton OBI enzyme-linked antibody @@ -18735,7 +18735,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 - A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. + A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ OBI developers @@ -18849,7 +18849,7 @@ https://www.doi.org/ - A cell specimen that contains only one cell. + A cell specimen that contains only one cell. Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl @@ -18880,7 +18880,7 @@ https://www.doi.org/ RNA Integrity Number calculation - A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. + A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. Chris Stoeckert, Bjoern Peters RIN calculation https://www.agilent.com/cs/library/applications/5989-1165EN.pdf @@ -18895,7 +18895,7 @@ https://www.doi.org/ RNA Integrity Number value specification - A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). + A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). Chris Stoeckert, Bjoern Peters RIN value specification OBI @@ -18924,7 +18924,7 @@ https://www.doi.org/ temperature value specification - A value specification that specifies the temperature of some thing. + A value specification that specifies the temperature of some thing. Chris Stoeckert OBI temperature value specification @@ -18952,7 +18952,7 @@ https://www.doi.org/ volume value specification - A value specification that specifies the volume of some thing. + A value specification that specifies the volume of some thing. Chris Stoeckert OBI volume value specification @@ -18982,7 +18982,7 @@ https://www.doi.org/ courier organization - An organization that delivers messages, packages, and mail. + An organization that delivers messages, packages, and mail. Chris Stoeckert, Helena Ellis courier https://en.wikipedia.org/wiki/Courier @@ -18998,7 +18998,7 @@ https://www.doi.org/ courier tracking number - A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. + A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -19013,7 +19013,7 @@ https://www.doi.org/ tissue section thickness - A length measurement datum that is the result of an assay measuring the thickness of a tissue section. + A length measurement datum that is the result of an assay measuring the thickness of a tissue section. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -19050,7 +19050,7 @@ https://www.doi.org/ molecular analysis facility organization An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. - An organization that provides molecular analysis service. + An organization that provides molecular analysis service. Chris Stoeckert, Helena Ellis MAF NCI BBRB, OBIB @@ -19070,7 +19070,7 @@ https://www.doi.org/ - A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. + A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 @@ -19083,7 +19083,7 @@ https://www.doi.org/ - 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. + 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 @@ -19097,7 +19097,7 @@ https://www.doi.org/ - An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. + An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. Rebecca Jackson DSH differential screening @@ -19165,7 +19165,7 @@ https://www.doi.org/ defined population inclusion criterion inclusion based on age, sex, and living region (rural area or specified city). - An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. + An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. Chris Stoeckert, Mathias Brochhausen MIABIS 2.0 https://github.com/obi-ontology/obi/issues/920 @@ -19251,7 +19251,7 @@ https://www.doi.org/ age since culture seeding measurement datum - An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). + An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). Stephen A. Fisher, Junhyong Kim, Dan Berrios age of culture age since culture seeding measurement datum @@ -19553,7 +19553,7 @@ https://www.doi.org/ "18-33 years old" - An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. + An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen https://github.com/obi-ontology/obi/issues/839 age group inclusion criterion @@ -19667,7 +19667,7 @@ https://www.doi.org/ 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. + 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 @@ -19683,7 +19683,7 @@ https://www.doi.org/ RNA extraction with polyA depletion - A RNA extraction process in which only RNAs lacking a polyA tail are retained + 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 @@ -19697,7 +19697,7 @@ https://www.doi.org/ machine learning - A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. + A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. Mark A. Miller https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN @@ -19711,7 +19711,7 @@ 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://github.com/TrisSN @@ -19725,7 +19725,7 @@ 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://github.com/TrisSN @@ -19738,7 +19738,7 @@ https://www.doi.org/ - 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. + 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 @@ -19759,7 +19759,7 @@ https://www.doi.org/ swab specimen - A specimen that is stored on a swab as the output of a collecting specimen with swab process. + A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI https://github.com/obi-ontology/obi/issues/910 @@ -19775,7 +19775,7 @@ https://www.doi.org/ collecting specimen with swab - A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). + A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 @@ -19790,7 +19790,7 @@ https://www.doi.org/ 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. + 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 @@ -19803,7 +19803,7 @@ https://www.doi.org/ 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. + An information content entity that contains information about a nationwide group of individuals. MIABIS Sarah Bost MIABIS contributors @@ -19817,7 +19817,7 @@ https://www.doi.org/ 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. + 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 @@ -19832,7 +19832,7 @@ https://www.doi.org/ Site-directed mutagenesis was used to prepare mutants of the Hypoxia-inducible factor-1 (HIF-1) alpha subunit to investigate the role of certain amino acids in hypoxia. (PMID:12393189) - An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. + An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. Rebecca Jackson url:https://www.ncbi.nlm.nih.gov/books/NBK21945/ https://github.com/obi-ontology/obi/issues/1058 @@ -19847,7 +19847,7 @@ https://www.doi.org/ Error-prone PCR was used to introduce amino acid mutations to the cAMP receptor protein (CRP) of E. coli to investigate strain engineering to improve osmotolerance for industrial requirements. (PMID:22179860) - An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. + An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. Rebecca Jackson PMID:15153637 https://github.com/obi-ontology/obi/issues/1058 @@ -19861,7 +19861,7 @@ https://www.doi.org/ - A genetic transformation which reduces the expression of a specific gene or genes in an organism. + A genetic transformation which reduces the expression of a specific gene or genes in an organism. Rebecca Jackson gene knock-down url:https://en.wikipedia.org/wiki/Gene_knockdown @@ -19881,7 +19881,7 @@ https://www.doi.org/ - A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. + A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. Rebecca Jackson RNA interference gene knockdown url:https://en.wikipedia.org/wiki/Gene_knockdown @@ -19897,7 +19897,7 @@ 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. - An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). + 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 @@ -19916,7 +19916,7 @@ https://www.doi.org/ - A specimen composed of an individual organism to be studied in an investigation. + 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 @@ -19931,7 +19931,7 @@ https://www.doi.org/ 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 @@ -19948,7 +19948,7 @@ https://www.doi.org/ - A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). + A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). Jie Zheng short interspersed elements PCR PMID: 12711348 @@ -19964,7 +19964,7 @@ https://www.doi.org/ - 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. + 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 @@ -19981,7 +19981,7 @@ https://www.doi.org/ - An electrophoresis that separates and characterize proteins based on reaction with antibodies. + An electrophoresis that separates and characterize proteins based on reaction with antibodies. Jie Zheng IEP https://en.wikipedia.org/wiki/Immunoelectrophoresis @@ -19997,7 +19997,7 @@ https://www.doi.org/ - 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. + 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 @@ -20012,7 +20012,7 @@ https://www.doi.org/ - 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. + 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 @@ -20028,7 +20028,7 @@ https://www.doi.org/ - 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. + 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 @@ -20044,7 +20044,7 @@ https://www.doi.org/ - An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. + 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 @@ -20059,7 +20059,7 @@ https://www.doi.org/ - An organism feature identification objective that aims to detect insecticide resistance of an insect. + 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 @@ -20075,7 +20075,7 @@ https://www.doi.org/ 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. + 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 @@ -20183,7 +20183,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - A categorical value specification in which the available categories were created with an explicit order. + A categorical value specification in which the available categories were created with an explicit order. https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet. @@ -20249,7 +20249,7 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - An ordinal value specification that indicates that either + An ordinal value specification that indicates that either a) an analyte or mesaurand is present in an evaluant, or b) that the amount of analyte/measurand detected is over some predetermined threshold. Mark Andrew Miller, ORCID:0000-0001-9076-6066 @@ -20287,7 +20287,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - 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. + 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 @@ -20300,7 +20300,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - 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. + 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 @@ -20313,7 +20313,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. + 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 @@ -20327,7 +20327,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre surveillance process - An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. + An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. Chris Stoeckert Shane Babcock, OBI https://github.com/obi-ontology/obi/issues/1181 @@ -20343,7 +20343,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cluster study group role A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound. - A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. + A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. Chris Stoeckert, Brianna Lindsay cluster study arm ClinEpiDB @@ -20358,7 +20358,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre compound study group role A compound study group consisting of geographically proximate households that share a common water source. - A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. + A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. Chris Stoeckert, Brianna Lindsay compound study arm ClinEpiDB @@ -20372,7 +20372,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre altitude measurement datum - A length measurement datum between a point at sea or ground level and some point above it. + A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum @@ -20386,7 +20386,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre duration of specimen collection Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration. - A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. + A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. specimen collection duration VEuPathDB specimen collection duration @@ -20415,7 +20415,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre material supplier - A person or organization that provides material supplies to other people or organizations. + A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier @@ -20429,7 +20429,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre prevalence of pathogen in specimens prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR - A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. + A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. Chris Stoeckert prevalence of pathogen VEuPathDB @@ -20444,7 +20444,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre prevalence of blood meal specimens from a host organism prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal. - A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. + A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. Chris Stoeckert host blood index VEuPathDB @@ -20459,7 +20459,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre presence of blood from host organism in blood meal specimen presence of blood meal host organism indicated by boolean values of yes or no. - A data item that indicates whether blood in a blood meal specimen came from a specified host organism. + A data item that indicates whether blood in a blood meal specimen came from a specified host organism. Chris Stoeckert presence of blood meal host organism VEuPathDB @@ -20483,7 +20483,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood meal source organism - An organism that is the source of a blood meal. + An organism that is the source of a blood meal. Chris Stoeckert blood meal host organism VEuPathDB @@ -20498,7 +20498,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood meal source role A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal. - A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. + A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. Will deprecate this term in VEuPathDB ontology once in OBI. Chris Stoeckert http://purl.obolibrary.org/obo/EUPATH_0000791 @@ -20511,7 +20511,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A role of a material entity realized in drawing an arthropod in the direction of the material. + A role of a material entity realized in drawing an arthropod in the direction of the material. John Judkins attractant IRO:0000034 @@ -20526,7 +20526,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. + An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 @@ -20540,7 +20540,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that has the objective of collecting gravid female arthropods. + An arthropod specimen collection process that has the objective of collecting gravid female arthropods. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 @@ -20554,7 +20554,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. + An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. John Judkins VSMO:0000514 https://github.com/obi-ontology/obi/issues/1302 @@ -20568,7 +20568,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection by aspiration that occurs in the daytime. + An arthropod specimen collection by aspiration that occurs in the daytime. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 @@ -20582,7 +20582,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection by aspiration that catches specimens resting inside a human house. + An arthropod specimen collection by aspiration that catches specimens resting inside a human house. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB @@ -20595,7 +20595,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that occurs while the arthropods land on a surface. + An arthropod specimen collection process that occurs while the arthropods land on a surface. John Judkins collection of landing insects VSMO:0001457 @@ -20610,7 +20610,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. + An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB @@ -20630,7 +20630,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre barcode target locus role - An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. + An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 @@ -20650,7 +20650,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre oligonucleotide primer set - A processed material that consists of oligonucleotides that bear a primer role. + A processed material that consists of oligonucleotides that bear a primer role. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 @@ -20663,7 +20663,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A data item that is about resistance to an insecticide. + A data item that is about resistance to an insecticide. John Judkins VEuPathDB insecticide resistance datum @@ -20685,7 +20685,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A data item that is the specified output of an organism detection assay. + A data item that is the specified output of an organism detection assay. John Judkins VEuPathDB organism detection datum @@ -20697,7 +20697,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. + A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system @@ -20710,7 +20710,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. + A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system @@ -20723,7 +20723,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Organization that undertakes a clinical study at some point in time. + Organization that undertakes a clinical study at some point in time. Chris Stoeckert Cristian Cocos Jie Zheng @@ -20737,7 +20737,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. + A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. John Judkins VEuPathDB sequencing protocol @@ -20755,7 +20755,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A protocol that specifies processes to fulfill a specimen collection objective. + A protocol that specifies processes to fulfill a specimen collection objective. John Judkins VEuPathDB specimen collection protocol @@ -20783,7 +20783,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A symbol that denotes a participant under investigation. + A symbol that denotes a participant under investigation. John Judkins VEuPathDB participant identifier @@ -20795,7 +20795,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A temperature measurement datum that is about an axilla. + A temperature measurement datum that is about an axilla. John Judkins VEuPathDB axillary temperature measurement datum @@ -20807,7 +20807,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A temperature measurement datum that is about an organism. + A temperature measurement datum that is about an organism. Chris Stoeckert Jie Zheng Penn Group @@ -20826,7 +20826,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - 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 @@ -20838,7 +20838,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An age since birth measurement datum at the time of subject enrollment. + An age since birth measurement datum at the time of subject enrollment. Jie Zheng Penn Group age since birth at time of enrollment @@ -20850,7 +20850,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An age since birth measurement datum at the time of a clinical visit. + An age since birth measurement datum at the time of a clinical visit. Chris Stoeckert Grant Dorsey Jie Zheng @@ -20865,7 +20865,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A data item that is about a collection of insects. + A data item that is about a collection of insects. John Judkins entomological measurement datum VEuPathDB @@ -20878,7 +20878,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A scalar measurement datum that is the result of measuring temperature. + A scalar measurement datum that is the result of measuring temperature. John Judkins VEuPathDB temperature measurement datum @@ -20891,7 +20891,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre extraction date - A time measurement datum that specifies when some material was extracted from an input material. + 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 @@ -20905,7 +20905,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre extraction duration time - A time measurement datum that is the result of measuring the duration of an extraction process. + 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 @@ -20919,7 +20919,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -20933,7 +20933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -20947,7 +20947,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre laboratory postal address - A postal address used as a directive to deliver something to a laboratory. + 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 @@ -20963,7 +20963,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -20989,7 +20989,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A complex of molecular entitites which is the result of an antibody binding to an antigen. + A complex of molecular entitites which is the result of an antibody binding to an antigen. Bjoern Peters Hector Guzman-Orozco IEDB @@ -21015,7 +21015,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope 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 @@ -21034,7 +21034,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A complex of molecular entities which is the result of a MHC molecule binding with a ligand. + A complex of molecular entities which is the result of a MHC molecule binding with a ligand. Bjorne Peters Hector Guzman-Orozco IEDB @@ -21048,7 +21048,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21062,7 +21062,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21077,7 +21077,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21090,7 +21090,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21104,7 +21104,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21120,7 +21120,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21134,7 +21134,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21149,7 +21149,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21162,7 +21162,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21175,7 +21175,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21188,7 +21188,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21203,7 +21203,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21222,7 +21222,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A binding datum that is expressed as a categorical value. + A binding datum that is expressed as a categorical value. IEDB qualitative binding datum IEDB @@ -21235,7 +21235,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A binding datum that is expressed using numbers. + A binding datum that is expressed using numbers. IEDB IEDB quantitative binding datum @@ -21262,7 +21262,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). + A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). Bjoern Peters Hector Guzman-Orozco IEDB @@ -21290,7 +21290,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). + A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). Bjoern Peters Hector Guzman-Orozco IEDB @@ -21309,7 +21309,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A blood harvesting process in which white blood cells are separated from a blood specimen. + 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 @@ -21321,7 +21321,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences. + An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences. Christian Stoeckert ORCID:0000-0002-5714-991X Jie Zheng ORCID:0000-0002-2999-0103 laboratory @@ -21338,7 +21338,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. + 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 @@ -21361,7 +21361,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of perforin during cytotoxic T cell degranulation. + The release of perforin during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21384,7 +21384,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of granzyme A during cytotoxic T cell degranulation. + The release of granzyme A during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21407,7 +21407,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of granzyme B during cytotoxic T cell degranulation. + The release of granzyme B during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21430,7 +21430,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of granulysin during cytotoxic T cell degranulation. + The release of granulysin during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21453,7 +21453,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The subject being scanned in an MRI study, and bearor of data derived from that study. + The subject being scanned in an MRI study, and bearor of data derived from that study. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" @@ -21479,7 +21479,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role. + An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" @@ -21495,7 +21495,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The NMR/MRI machine protocol about the radiofrequency pulse sequence. + The NMR/MRI machine protocol about the radiofrequency pulse sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" @@ -21515,7 +21515,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. + A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 organism diagnostic process @@ -21533,7 +21533,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. + A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 diagnosis of an organism @@ -21556,7 +21556,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. + A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific XCL1 release by T cells @@ -21614,7 +21614,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. + A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. The Mother and Child Health and Education Trust mid-upper arm circumference datum @@ -21667,7 +21667,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The administration of a malignant cell to a host. + The administration of a malignant cell to a host. Hector Guzman-Orozco IEDB tumor challenge @@ -21679,7 +21679,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A preparative chromatography in which material components are separated in a liquid solution. + A preparative chromatography in which material components are separated in a liquid solution. Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1685 @@ -21692,7 +21692,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay. + A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay. Bjoern Peters Hector Guzman-Orozco OBI @@ -21706,7 +21706,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay. + A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay. Bjoern Peters Hector Guzman-Orozco OBI @@ -21733,7 +21733,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Staining using carboxyfluorescein succinimidyl ester. + Staining using carboxyfluorescein succinimidyl ester. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 carboxyfluorescein succinimidyl ester staining @@ -21745,7 +21745,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Staining using Annexin V to detect apoptotic cells. + Staining using Annexin V to detect apoptotic cells. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 Annexin V staining @@ -21763,7 +21763,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. + A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. Sebastian Duesing CADI chronic allograft damage index score @@ -21775,7 +21775,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies the degree of function of a critically ill patient's organs. + A clinical data item that quantifies the degree of function of a critically ill patient's organs. Sebastian Duesing SOFA score https://en.wikipedia.org/wiki/SOFA_score @@ -21794,7 +21794,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. + A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. Sebastian Duesing MD global, PGA physician's global assessment of disease activity @@ -21806,7 +21806,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. + A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. Sebastian Duesing HLA mismatch count, HLA mismatch human leukocyte antigen mismatch count @@ -21829,7 +21829,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An objective specification that is fulfilled by reducing the severity of a disease in a particular organism. + An objective specification that is fulfilled by reducing the severity of a disease in a particular organism. Sebastian Duesing disease severity reduction objective @@ -21840,7 +21840,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An objective specification that is fulfilled by preventing the development of a disease in a particular organism. + An objective specification that is fulfilled by preventing the development of a disease in a particular organism. Sebastian Duesing disease prevention objective @@ -21874,7 +21874,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms. + An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms. Sebastian Duesing disease prevalence reduction objective @@ -21917,7 +21917,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A purification to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC protein complex, while others contain impurities and are not of interest. + A purification to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing antibody purification of MHC protein complex @@ -21929,7 +21929,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. + A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. Sebastian Duesing https://pubmed.ncbi.nlm.nih.gov/7636775/ DOI: 10.1016/0022-3999(94)00125-o multidimensional fatigue inventory score @@ -21952,7 +21952,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre albumin-free serum - A blood serum specimen that contains no albumin. + A blood serum specimen that contains no albumin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/493 Philippe Rocca-Serra @@ -21989,7 +21989,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fasting Pre-test fasting is required or recommended for several blood tests, including glucose and C-peptide tests. 8–12 hours is typical for fasting duration. - A planned process in which an organism drinks only water and does not eat for a specified period of time. + A planned process in which an organism drinks only water and does not eat for a specified period of time. Sebastian Duesing A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. https://github.com/obi-ontology/obi/issues/494 @@ -22004,7 +22004,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Overnight fasting commonly occurs prior to a blood draw scheduled in the morning. - A fasting with a duration of 8–12 hours, typically occurring overnight. + A fasting with a duration of 8–12 hours, typically occurring overnight. Sebastian Duesing A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. https://github.com/obi-ontology/obi/issues/494 @@ -22024,7 +22024,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats. + An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats. Sebastian Duesing https://github.com/obi-ontology/obi/issues/494 Philippe Rocca-Serra @@ -22056,7 +22056,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument. + An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument. Sebastian Duesing least count https://en.wikipedia.org/wiki/Least_count @@ -22073,7 +22073,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -22398,7 +22398,7 @@ This issue is outside the scope of OBI. 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 cell culture sample @@ -22436,7 +22436,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from 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.' consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. PERSON:Matthew Brush @@ -22591,7 +22591,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ glucose in solution Glucose present in blood - A scattered aggregate of glucose molecules in a liquid + A scattered aggregate of glucose molecules in a liquid PERSON: Jie Zheng glucose molecules glucose in solution @@ -22682,7 +22682,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ geometric mean calculation - A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). + A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). Mathias Brochhausen PERSON: Mathias Brochhausen A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). @@ -23313,7 +23313,7 @@ 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 + 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 @@ -23334,7 +23334,7 @@ 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 - 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 + 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 @@ -23355,7 +23355,7 @@ 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 - Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method + 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 @@ -23416,7 +23416,7 @@ 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) - 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 @@ -23599,7 +23599,7 @@ 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) - 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 @@ -23939,7 +23939,7 @@ 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 - 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 @@ -24039,7 +24039,7 @@ 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 @@ -24272,7 +24272,7 @@ allows correct classification of FWER dt survival analysis objective 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 + 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 @@ -24294,7 +24294,7 @@ 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 @@ -24332,7 +24332,7 @@ 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) + 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 @@ -24353,7 +24353,7 @@ allows correct classification of FWER dt 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 + 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. @@ -24371,7 +24371,7 @@ allows correct classification of FWER dt 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. + a data transformation objective of determining the concordance or agreement between human judges. Person:Alan Ruttenberg Person:Helen Parkinson inter-rater agreement @@ -24405,7 +24405,7 @@ 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 @@ -24480,7 +24480,7 @@ 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 is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. + 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 @@ -24692,7 +24692,7 @@ 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 @@ -25400,7 +25400,7 @@ information_encoding 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. + 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 @@ -25509,7 +25509,7 @@ 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. - 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. + 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 @@ -25530,7 +25530,7 @@ information_encoding 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). + 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 @@ -25550,7 +25550,7 @@ information_encoding 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. + 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 @@ -25570,7 +25570,7 @@ information_encoding 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. + 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 @@ -25653,7 +25653,7 @@ 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. + 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 @@ -25682,7 +25682,7 @@ 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' + 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 @@ -25703,7 +25703,7 @@ 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. + 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 @@ -25736,7 +25736,7 @@ 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 @@ -25769,7 +25769,7 @@ 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. + 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 @@ -25798,7 +25798,7 @@ 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). + 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 @@ -26024,7 +26024,7 @@ to create a common base for comparisons. 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. + 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 @@ -26090,7 +26090,7 @@ 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 - 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 @@ -26162,7 +26162,7 @@ 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 - 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 @@ -26313,7 +26313,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26338,7 +26338,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26370,7 +26370,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26402,7 +26402,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26422,7 +26422,7 @@ class labels for these objects. The resulting predictor can be used to attach cl survival analysis data transformation - A data transformation which has the objective of performing survival analysis. + A data transformation which has the objective of performing survival analysis. James Malone PERSON: James Malone survival analysis data transformation @@ -26442,7 +26442,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26459,7 +26459,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26473,7 +26473,7 @@ 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 - is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. + 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 @@ -26493,7 +26493,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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 @@ -26516,7 +26516,7 @@ determinations of compounds. 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. + 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 @@ -26530,7 +26530,7 @@ determinations of compounds. ANOVA - A statistical hypothesis test in which the means of several groups are all equal. + A statistical hypothesis test in which the means of several groups are all equal. James Malone ANOVA @@ -26630,7 +26630,7 @@ 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 - a role which inheres in some molecular entity realized during the process of buffering + a role which inheres in some molecular entity realized during the process of buffering Person:Helen Parkinson Person:Philippe Rocca-Serra buffer @@ -26779,7 +26779,7 @@ 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. - An 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. + An 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 @@ -26803,7 +26803,7 @@ 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 - a role that borne by an organism and realized by some group randomization process + a role that borne by an organism and realized by some group randomization process Person:Helen Parkinson Philippe Rocca-Serra randomized group participant role @@ -26895,7 +26895,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 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 + 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 @@ -26916,7 +26916,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 edited document The OBI manuscript is (much) edited imformation - A document which is the output of a document editing process + A document which is the output of a document editing process Person:Bjoern Peters Philippe Rocca-Serra edited document @@ -26947,7 +26947,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 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 + A material entity that has been going through a process of being put into solution Person:Bjoern Peters Philippe Rocca-Serra dissolved material entity @@ -26968,7 +26968,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 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 @@ -27699,7 +27699,7 @@ 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. + 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 @@ -28102,7 +28102,7 @@ defines and states the requirements (positive or negative) for an entity to be c 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. + 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: @@ -28776,7 +28776,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ 'establishing cell culture' - a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). + a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. @@ -30070,7 +30070,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30084,7 +30084,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30098,7 +30098,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30295,7 +30295,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30310,7 +30310,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30354,7 +30354,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30369,7 +30369,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30384,7 +30384,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30419,7 +30419,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30434,7 +30434,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30448,7 +30448,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30462,7 +30462,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30507,7 +30507,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30531,7 +30531,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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. @@ -30559,7 +30559,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30629,7 +30629,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30668,7 +30668,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30721,7 +30721,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30760,7 +30760,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30807,7 +30807,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30934,7 +30934,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31251,7 +31251,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31287,7 +31287,7 @@ 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. - 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 @@ -31322,7 +31322,7 @@ 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. - 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 @@ -31344,7 +31344,7 @@ 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. - A material entity that is added to another material entity in an “adding a material entity into a target” process. + A material entity that is added to another material entity in an “adding a material entity into a target” 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 @@ -31366,7 +31366,7 @@ 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. - A material entity that receives the addition of another material entity in an “adding a material entity into a target” process. + A material entity that receives the addition of another material entity in an “adding a material entity into a target” 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 @@ -31394,7 +31394,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31424,7 +31424,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31438,7 +31438,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31739,7 +31739,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it allergen Birch pollen is an allergen - A material entity bearing the disposition to cause an allergic reaction + A material entity bearing the disposition to cause an allergic reaction IEDB IEDB allergen @@ -31852,7 +31852,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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) + 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 @@ -31868,7 +31868,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ - A specimen that has been fixed in formalin and embedded in paraffin. + A specimen that has been fixed in formalin and embedded in paraffin. MIABIS formalin-fixed paraffin-embeded specimen @@ -32520,7 +32520,7 @@ realizes some 'host of immune response role' GenePattern module SVM - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + 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 @@ -32566,7 +32566,7 @@ realizes some 'host of immune response role' GenePattern module KMeansClustering - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + 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 @@ -32592,7 +32592,7 @@ realizes some 'host of immune response role' 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 is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation @@ -32603,7 +32603,7 @@ realizes some 'host of immune response role' 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. + 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 @@ -32628,7 +32628,7 @@ realizes some 'host of immune response role' GenePattern module KNN - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN @@ -32641,7 +32641,7 @@ realizes some 'host of immune response role' GenePattern module HierarchicalClustering - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + 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 @@ -32666,7 +32666,7 @@ realizes some 'host of immune response role' GenePattern module PCA - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + 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 @@ -32691,7 +32691,7 @@ realizes some 'host of immune response role' GenePattern HeatMapViewer data visualization - The GenePattern process of generating Heat Maps from clustered data. + The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization @@ -32703,7 +32703,7 @@ realizes some 'host of immune response role' GenePattern HierarchicalClusteringViewer data visualization - The GenePattern process of generating hierarchical clustering visualization from clustered data. + The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization @@ -32716,7 +32716,7 @@ realizes some 'host of immune response role' GenePattern module HeatMapViewer - A GenePattern software module which is used to generate a heatmap view of data. + A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer @@ -32729,7 +32729,7 @@ realizes some 'host of immune response role' GenePattern module HierarchicalClusteringViewer - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index cc5b8e9d..aed4b76d 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique objective associated axiom -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C % OBI:0000281 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 equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe'))) OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism 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 Person:Bjoern Peters equivalent administering substance in vivo peritoneum OBI:0000837 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 equivalent oral administration pill ('has_specified_input' some 'pill') diff --git a/src/ontology/templates/antibody-purification.tsv b/src/ontology/templates/antibody-purification.tsv index f5b3d877..7227c734 100644 --- a/src/ontology/templates/antibody-purification.tsv +++ b/src/ontology/templates/antibody-purification.tsv @@ -1,5 +1,5 @@ id rdfs label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent output -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C has_specified_output some % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C has_specified_output some % OBI:0003616 antibody purification of MHC class I protein complex An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC protein complex MHC class I protein complex OBI:0003617 antibody purification of human MHC class I protein complex An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC class I protein complex human MHC class I protein complex OBI:0003618 antibody purification of HLA protein complex with A2 serotype An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of human MHC class I protein complex HLA protein complex with A2 serotype diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 8679701b..47c9115b 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class material processing technique detection technique evaluant measurand analyte device reagent molecular label input output target entity target context objective associated axioms -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('measurand role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some ('analyte role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some ('molecular label role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C achieves_planned_objective some % C % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('measurand role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some ('analyte role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C (has_specified_input some %) and (realizes some ('molecular label role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C achieves_planned_objective some % C % CHMO:0000087 fluorescence microscopy assay fluorescence imaging|fluorescence microscopic imaging|FM 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. CHMO subclass light microscopy assay ('material entity' and ('bearer of' some fluorescence)) CHMO:0000089 confocal fluorescence microscopy assay CLSM|confocal fluorescence imaging|confocal laser scanning fluorescence microscopy|confocal laser scanning microscopy|confocal-laser scanning microscopy|fluorescence confocal microscopy|fluorescence confocal scanning laser microscopy|LSCM|scanning 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. CHMO subclass microscopy assay CHMO:0000102 light microscopy assay light microscopy|OM|optical microscopy Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. CHMO subclass microscopy assay diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv index 40c3371d..7e8c0c84 100644 --- a/src/ontology/templates/biobank-specimens.tsv +++ b/src/ontology/templates/biobank-specimens.tsv @@ -1,5 +1,5 @@ -ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type specimen collection process gross anatomical part collection process input URI -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C specimen and (is_specified_output_of some %) C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C specimen and (is_specified_output_of some ('specimen collection process' and has_specified_input some %)) +ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type specimen collection process gross anatomical part collection process input URI +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C specimen and (is_specified_output_of some %) C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C specimen and (is_specified_output_of some ('specimen collection process' and has_specified_input some %)) OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism amniotic fluid UBERON_0000173 OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism bile UBERON_0001970 OBI:0002502 cerebrospinal fluid specimen ready for release A specimen that is derived from cerbrospinal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism cerebrospinal fluid UBERON_0001359 diff --git a/src/ontology/templates/biopsy.tsv b/src/ontology/templates/biopsy.tsv index 5312a101..3d8e352c 100644 --- a/src/ontology/templates/biopsy.tsv +++ b/src/ontology/templates/biopsy.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class material anatomical entity input device output entity -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'has_specified_input' some % C 'has_specified_input' some % C 'has_specified_output' some % +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'has_specified_input' some % C 'has_specified_input' some % C 'has_specified_output' some % OBI:0002650 biopsy ready for release 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. https://en.wikipedia.org/wiki/Biopsy Biopsy of a potentially cancerous mole. Nicole Vasilevsky|Damion Dooley subclass collecting specimen from organism material anatomical entity device pre-mortem specimen OBI:0002651 image guided biopsy ready for release image-guided biopsy|imaging guided biopsy|image guided needle biopsy A biopsy which uses an imaging procedure to guide a needle 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. Damion Dooley subclass needle biopsy OBI:0002652 computed tomography assisted biopsy ready for release Computed Tomography Assisted Biopsy|CT Guided Biopsy|CT Assisted Biopsy|Computed Tomography-Guided Needle Biopsy A needle biopsy guided by real-time computed tomography (CT) scan images. 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. Damion Dooley subclass image guided biopsy computed tomography scanner diff --git a/src/ontology/templates/data-sets.tsv b/src/ontology/templates/data-sets.tsv index 95fb8ba3..d1551234 100644 --- a/src/ontology/templates/data-sets.tsv +++ b/src/ontology/templates/data-sets.tsv @@ -1,5 +1,5 @@ ontology ID label has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class is about is specified output of has member -ID A rdfs:label AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=, A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'is about' some % C is_specified_output_of some % C 'has member' some % +ID A rdfs:label AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=, A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE CI C 'is about' some % C is_specified_output_of some % C 'has member' some % OBI:0003327 image data set A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. The output produced by a digital imaging technique, such as microscopy, MRI, or CT. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra"",https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data set entity OBI:0003328 magnetic resonance image data set An image data set whose information content originates from some MR imaging assay and is about some MRI participant. MRI at a Glance, ISBN 10: 1119053552 The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra"",https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set magnetic resonance imaging participant OBI:0003331 raw image data set An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. The untransformed (""k-space"") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra"",https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"",https://orcid.org/0000-0002-1604-3078 ""Alan Ruttenberg"" https://github.com/obi-ontology/obi/issues/1481 subclass image data set diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv index 69694ebf..dbe7caa6 100644 --- a/src/ontology/templates/data-transformations.tsv +++ b/src/ontology/templates/data-transformations.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note term tracker item logical type parent class input output objective associated axioms -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A term tracker item CLASS_TYPE C % C has_specified_input some % C has_specified_output some % C achieves_planned_objective some % C % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A term tracker item CLASS_TYPE C % C has_specified_input some % C has_specified_output some % C achieves_planned_objective some % C % OBI:0003355 image data set analysis The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data transformation image data set OBI:0003356 raw magnetic resonance image data set reconstruction A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. A Fourier transform of raw ""k-space"" data produced into an image data set that represents the anatomical structure of the tissue examined. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set analysis raw magnetic resonance image data set reconstructed magnetic resonance image data set OBI:0003647 tandem mass spectrometry analysis tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'tandem mass spectrometry assay') diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 9e1b4426..ee8e777e 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class function has part part of manufactured by associated axioms -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=| +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=| OBI:0000038 chromatography column chromatography column metadata incomplete 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. http://en.wikipedia.org/wiki/Column_chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device ('material separation function' and ('realized in' only 'preparative chromatography')) container OBI:0000041 pump valve switch pump valve switch metadata incomplete A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. OBI OBI Instrument branch FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument device mechanical function OBI:0000048 chromatography device chromatography device metadata complete chromatography instrument 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. http://en.wikipedia.org/wiki/Chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device contain function|environment control function|measure function|material separation function diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index 728f93dd..bdd2534c 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -1,5 +1,5 @@ Ontology ID label editor preferred term has curation status alternative term IEDB alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class material processing technique detection technique reagent input output MHC source target entity target context unit -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_input some (% and ('has part' some 'MHC protein complex')) C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C has_specified_output some ('has measurement unit label' value %) +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_input some (% and ('has part' some 'MHC protein complex')) C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C has_specified_output some ('has measurement unit label' value %) OBI:0001194 ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells TGFb release|ELISPOT An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('transforming growth factor beta production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001196 cytometric bead array assay measuring epitope specific IP-10 production by T cells CXCL10/IP-10 release|cytometric bead array A cytometric bead array assay that detects IP-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('IP-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) OBI:0001198 assay measuring epitope specific interleukin-27 production by T cells IL-27 release|biological activity A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interleukin-27 production' and ('process is result of' some 'MHC:epitope complex binding to TCR')) diff --git a/src/ontology/templates/medical-history.tsv b/src/ontology/templates/medical-history.tsv index d33ec5b9..3dafc77d 100644 --- a/src/ontology/templates/medical-history.tsv +++ b/src/ontology/templates/medical-history.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % OBI:0002368 clinical history of cancer A clinical history in which there is a diagnosis of cancer. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history OBI:0002369 clinical history devoid of cancer clinical history of no cancer A clinical history in which there was no diagnosis of cancer. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history OBI:0002370 unknown clinical history of cancer A clinical history in which it is not known whether there was a diagnosis of cancer. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 3cb52b68..39f14605 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term IEDB Alternative Terms definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class obsolete obsolescence reason replacement term Randi notes on obsolescence -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % AT deprecated^^xsd:boolean AI has obsolescence reason AI term replaced by +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % AT deprecated^^xsd:boolean AI has obsolescence reason AI term replaced by OBI:0000050 obsolete_platform metadata incomplete 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 subclass Obsolete Class true IAO:0000103 OBI:0000100 obsolete_role of being first subject treated metadata complete 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 OBI Rat 1A; first enrolled patient to receive treatment Role Branch subclass Obsolete Class true IAO:0000103 OBI:0000109 obsolete biological vector role metadata complete 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. OBI and Wikipedia 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 GROUP: Role Branch subclass Obsolete Class true IAO:0000103 diff --git a/src/ontology/templates/organizations.tsv b/src/ontology/templates/organizations.tsv index d0f6070e..dd3c57c6 100644 --- a/src/ontology/templates/organizations.tsv +++ b/src/ontology/templates/organizations.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type type -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE TYPE SPLIT=| +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE TYPE SPLIT=| OBI:0000462 Affymetrix Affymetrix An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix supplied microarray manufacturer|material supplier OBI:0000752 Thermo Thermo Philippe Rocca-Serra manufacturer OBI:0000753 Waters Waters Philippe Rocca-Serra manufacturer diff --git a/src/ontology/templates/physical-examination.tsv b/src/ontology/templates/physical-examination.tsv index 8df08f5f..7aeb49b3 100644 --- a/src/ontology/templates/physical-examination.tsv +++ b/src/ontology/templates/physical-examination.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class detection technique evaluant device input output anatomical site assessed biological trait -ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some (% and 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) OBI:0003501 functional assessment of individual A physical examination of an organism's ability to perform functional activities. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass physical examination of an organism OBI:0003502 facial atrophy assessment An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual facial muscle facial muscle performance OBI:0003503 tongue atrophy assessment An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual tongue facial muscle performance diff --git a/src/ontology/templates/sample-collection.tsv b/src/ontology/templates/sample-collection.tsv index 2248c9d2..c2731ddf 100644 --- a/src/ontology/templates/sample-collection.tsv +++ b/src/ontology/templates/sample-collection.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class specimen type -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C has_specified_output some (% and 'has role' some 'specimen role') +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C has_specified_output some (% and 'has role' some 'specimen role') OBI:0002904 adult arthropod specimen collection process collection of adults A live arthropod specimen collection process in which the arthropods are in the adult stage. MIRO:30000052 John Judkins https://github.com/obi-ontology/obi/issues/1217 live arthropod specimen collection process OBI:0002905 animal-biting arthropod specimen collection by aspiration animal biting catch An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. MIRO:30000012 John Judkins https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection by aspiration OBI:0002906 animal-biting outdoor arthropod specimen collection by aspiration animal biting catch - outdoors An animal-biting arthropod specimen collection by aspiration that occurs outside a building. MIRO:30000014 John Judkins https://github.com/obi-ontology/obi/issues/1217 animal-biting arthropod specimen collection by aspiration diff --git a/src/ontology/templates/sequence-analysis.tsv b/src/ontology/templates/sequence-analysis.tsv index afd3d4a7..9fb69b27 100644 --- a/src/ontology/templates/sequence-analysis.tsv +++ b/src/ontology/templates/sequence-analysis.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class output input input of output of objective -ID A rdfs:label A editor preferred term AL has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has_specified_output' some % C 'has_specified_input' some % C is_specified_input_of some % C is_specified_output_of some % C achieves_planned_objective some % +ID A rdfs:label A editor preferred term AL has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has_specified_output' some % C 'has_specified_input' some % C is_specified_input_of some % C is_specified_output_of some % C achieves_planned_objective some % OBI:0002565 adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios subclass sequence trimming adapter-trimmed sequence data 'adapter sequence data' OBI:0002566 file merge A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios subclass data transformation OBI:0002567 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 subclass sequence analysis data transformation aligned sequence data sequence data diff --git a/src/ontology/templates/specimen-assay-data.tsv b/src/ontology/templates/specimen-assay-data.tsv index 6b48dbdd..84caaf7d 100644 --- a/src/ontology/templates/specimen-assay-data.tsv +++ b/src/ontology/templates/specimen-assay-data.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item axiom -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item EC % +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item EC % OBI:0003243 blood assay datum A data item that is the specified output of a blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'blood assay') OBI:0003244 blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'blood microbiology assay') OBI:0003245 feces assay datum A data item that is the specified output of a feces assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'feces assay') diff --git a/src/ontology/templates/study-designs.tsv b/src/ontology/templates/study-designs.tsv index 94e43c45..50ae1a83 100644 --- a/src/ontology/templates/study-designs.tsv +++ b/src/ontology/templates/study-designs.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class objective independent variable dependent variable assay associated superclasses associated equivalent classes -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ('study design independent variable' and ('is about' some %)) SPLIT=| C 'has part' some ('study design dependent variable' and ('is about' some %)) SPLIT=| C 'is concretized as' some ('realized in' some ('has part' some %)) SPLIT=| SC % SPLIT=| EC % SPLIT=| +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has part' some % SPLIT=| C 'has part' some ('study design independent variable' and ('is about' some %)) SPLIT=| C 'has part' some ('study design dependent variable' and ('is about' some %)) SPLIT=| C 'is concretized as' some ('realized in' some ('has part' some %)) SPLIT=| SC % SPLIT=| EC % SPLIT=| OBI:0000115 intervention design intervention design pending final vetting 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. OBI branch derived 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. Philppe Rocca-Serra equivalent study design study intervention OBI:0000951 compound treatment design compound treatment design metadata complete an intervention design in which the treatment is the administration of a compound MO_555 compound_treatment_design PERSON: Bjoern Peters This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. subclass study design ('study intervention' and 'administration of material to specimen') OBI:0000985 growth condition intervention design growth condition intervention design metadata complete A study design in which the independent variable is the environmental condition in which the specimen is growing MO_588 growth_condition_design PERSON: Bjoern Peters subclass intervention design study intervention|growth environment diff --git a/src/ontology/templates/value-specifications.tsv b/src/ontology/templates/value-specifications.tsv index 0344a1bd..adeeb7d4 100644 --- a/src/ontology/templates/value-specifications.tsv +++ b/src/ontology/templates/value-specifications.tsv @@ -1,5 +1,5 @@ ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type type parent class -ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE TYPE C % +ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE TYPE C % OBI:0002199 reason for lack of data item An information content entity that provides an explanation why a data item is not provided. OBI cannot be assessed, not applicable, unknown Chris Stoeckert, Helena Ellis NCI BBRB subclass information content entity OBI:0002200 cannot be assessed determination cannot be assessed A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass reason for lack of data item OBI:0002201 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. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass planned process From 3ed2ef576e7fe1673a72a8615fca5a1d08bd766d Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 27 Jun 2024 10:59:08 -0500 Subject: [PATCH 2/3] Update modules --- src/ontology/modules/administration.owl | 76 +- .../modules/antibody-purification.owl | 62 +- src/ontology/modules/biobank-specimens.owl | 204 +-- src/ontology/modules/biopsy.owl | 26 +- src/ontology/modules/data-sets.owl | 290 ++-- src/ontology/modules/data-transformations.owl | 4 +- src/ontology/modules/devices.owl | 1178 ++++++++--------- src/ontology/modules/epitope-assays.owl | 1080 +++++++-------- src/ontology/modules/medical-history.owl | 136 +- src/ontology/modules/obsolete.owl | 124 +- src/ontology/modules/organizations.owl | 20 +- src/ontology/modules/physical-examination.owl | 78 +- src/ontology/modules/sample-collection.owl | 38 +- src/ontology/modules/sequence-analysis.owl | 48 +- src/ontology/modules/specimen-assay-data.owl | 94 +- src/ontology/modules/study-designs.owl | 200 +-- src/ontology/modules/value-specifications.owl | 344 ++--- 17 files changed, 2001 insertions(+), 2001 deletions(-) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index c0141b5e..0ad3c632 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -177,7 +177,7 @@ 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 + 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 @@ -222,7 +222,7 @@ 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 + The administration of a substance into the peritoneum of an organism Person:Bjoern Peters intraperitoneal administration @@ -270,7 +270,7 @@ oral ingestion of pill - An adding a material entity to target with the entity is a pill and the target is the mouth + 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 @@ -323,7 +323,7 @@ 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 + 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 @@ -368,7 +368,7 @@ 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 + 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 @@ -400,7 +400,7 @@ oral administration - An administering substance in vivo into the mouth of an organism + An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot oral administration @@ -446,7 +446,7 @@ 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 + 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 @@ -478,7 +478,7 @@ intranasal mucosal administration - The administration of a substance into the intranasal mucosis of an organism + The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot intranasal mucosal administration @@ -524,7 +524,7 @@ 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 + 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 @@ -553,7 +553,7 @@ 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. + 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 @@ -582,7 +582,7 @@ antibiotic administration process - Administering substance in vivo where an antibiotic substance is administered to a living organism. + Administering substance in vivo where an antibiotic substance is administered to a living organism. Chris Stoeckert Cristian Cocos Jie Zheng @@ -602,7 +602,7 @@ - An administration of substance in vivo with the intention to induce disease in the organism. + An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB administering substance in vivo to cause disease @@ -628,7 +628,7 @@ - An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. + An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB administering substance in vivo to reduce or prevent disease @@ -641,7 +641,7 @@ in vivo challenge - The administration of a challenge to a live host. + The administration of a challenge to a live host. Hector Guzman-Orozco IEDB in vivo challenge @@ -669,7 +669,7 @@ - An administration of a substance into the stomach of an organism. + An administration of a substance into the stomach of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intragastric administration @@ -697,7 +697,7 @@ - An administration of a substance into the colon of an organism. + An administration of a substance into the colon of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intracolonic administration @@ -725,7 +725,7 @@ - An administration of a substance into the vagina of an organism. + An administration of a substance into the vagina of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 vaginal administration @@ -753,7 +753,7 @@ - An administration of a substance onto the surface of the skin of an organism. + An administration of a substance onto the surface of the skin of an organism. Sebastian Duesing percutaneous administration transcutaneous administration @@ -783,7 +783,7 @@ - An administration of a substance to the cervix of an organism. + An administration of a substance to the cervix of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 cervical administration @@ -811,7 +811,7 @@ - An administration of a substance to the conjunctiva of an organism. + An administration of a substance to the conjunctiva of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 conjunctival administration @@ -839,7 +839,7 @@ - An administration of a substance into the trachea of an organism. + An administration of a substance into the trachea of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intratracheal administration @@ -867,7 +867,7 @@ - An administration of a substance into the amnion of an organism. + An administration of a substance into the amnion of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intra-amniotic administration @@ -895,7 +895,7 @@ - An administration of a substance into the artery of an organism. + An administration of a substance into the artery of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intra-arterial administration @@ -923,7 +923,7 @@ - An administration of a substance into the cerebrum of an organism. + An administration of a substance into the cerebrum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intracerebral administration @@ -951,7 +951,7 @@ - An administration of a substance into the cranium of an organism. + An administration of a substance into the cranium of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intracranial administration @@ -979,7 +979,7 @@ - An administration of a substance into the epidermis of an organism. + An administration of a substance into the epidermis of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intraepidermal administration @@ -1012,7 +1012,7 @@ - An administration of a substance into the lymphatic system of an organism. + An administration of a substance into the lymphatic system of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intralymphatic administration @@ -1040,7 +1040,7 @@ - An intralymphatic administration in which the substance is administered into a lymph node. + An intralymphatic administration in which the substance is administered into a lymph node. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 lymph node administration @@ -1068,7 +1068,7 @@ - An administration of a substance into the urethra of an organism. + An administration of a substance into the urethra of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 urethral administration @@ -1102,7 +1102,7 @@ - An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. + An intraepidermal administration in which the skin is scratched before the substance is administered to the skin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 skin scarification administration @@ -1130,7 +1130,7 @@ - An adminstration of a substance into the uterus of an organism. + An adminstration of a substance into the uterus of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intrauteral administration @@ -1158,7 +1158,7 @@ - An intra-arterial administration in which the substance is administered into the carotid artery. + An intra-arterial administration in which the substance is administered into the carotid artery. Sebastian Duesing i.c. i.c. administration @@ -1188,7 +1188,7 @@ - An administration of a substance to the eye of an organism. + An administration of a substance to the eye of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intraocular administration @@ -1216,7 +1216,7 @@ - An administration of a substance into the placenta of an organism. + An administration of a substance into the placenta of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intraplacental administration @@ -1244,7 +1244,7 @@ - An administration of a substance into the rectum of an organism. + An administration of a substance into the rectum of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intrarectal administration @@ -1272,7 +1272,7 @@ - An administration of a substance into the spleen of an organism. + An administration of a substance into the spleen of an organism. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1703 intrasplenic administration @@ -1306,7 +1306,7 @@ - An administration of a substance into a tumor of an organism. + An administration of a substance into a tumor of an organism. Sebastian Duesing intratumoral administration @@ -1364,7 +1364,7 @@ administration in vivo with infectious agent - is an administration of an infectious agent to a host organism + is an administration of an infectious agent to a host organism IEDB IEDB administration in vivo with infectious agent diff --git a/src/ontology/modules/antibody-purification.owl b/src/ontology/modules/antibody-purification.owl index 6f796e67..2bdaa098 100644 --- a/src/ontology/modules/antibody-purification.owl +++ b/src/ontology/modules/antibody-purification.owl @@ -286,7 +286,7 @@ - An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -309,7 +309,7 @@ - An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -332,7 +332,7 @@ - An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -355,7 +355,7 @@ - An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A24 serotype, while others contain impurities and are not of interest. + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A24 serotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -385,7 +385,7 @@ - An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype, while others contain impurities and are not of interest. + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -408,7 +408,7 @@ - An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A29 serotype, while others contain impurities and are not of interest. + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A29 serotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -431,7 +431,7 @@ - An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with B27 serotype, while others contain impurities and are not of interest. + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with B27 serotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -454,7 +454,7 @@ - An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-C protein complex, while others contain impurities and are not of interest. + An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-C protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -477,7 +477,7 @@ - An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -500,7 +500,7 @@ - An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -523,7 +523,7 @@ - An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of rat MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of rat MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -546,7 +546,7 @@ - An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -569,7 +569,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex, while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -592,7 +592,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Db protein complex, while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Db protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -615,7 +615,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Kd protein complex, while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Kd protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -646,7 +646,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -676,7 +676,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex and/or H2-Kd protein complex while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex and/or H2-Kd protein complex while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -706,7 +706,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -737,7 +737,7 @@ - An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse H2-Kb protein complex, H2-Ks protein complex, and/or H2-Kq protein complex while others contain impurities and are not of interest. + An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse H2-Kb protein complex, H2-Ks protein complex, and/or H2-Kq protein complex while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -768,7 +768,7 @@ - An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -791,7 +791,7 @@ - An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class II protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class II protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -814,7 +814,7 @@ - An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class II protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class II protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -837,7 +837,7 @@ - An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class II protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class II protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -860,7 +860,7 @@ - An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DP protein complex, while others contain impurities and are not of interest. + An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DP protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -883,7 +883,7 @@ - An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DR protein complex, while others contain impurities and are not of interest. + An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DR protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -906,7 +906,7 @@ - An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with DQ3 serotype, while others contain impurities and are not of interest. + An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with DQ3 serotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -929,7 +929,7 @@ - An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex, while others contain impurities and are not of interest. + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -952,7 +952,7 @@ - An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IA protein complex, while others contain impurities and are not of interest. + An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IA protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -975,7 +975,7 @@ - An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAg7 protein complex, while others contain impurities and are not of interest. + An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAg7 protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -998,7 +998,7 @@ - An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAd protein complex, while others contain impurities and are not of interest. + An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAd protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita @@ -1028,7 +1028,7 @@ - An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype, while others contain impurities and are not of interest. + An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing Randi Vita diff --git a/src/ontology/modules/biobank-specimens.owl b/src/ontology/modules/biobank-specimens.owl index a10afdaf..01aa098a 100644 --- a/src/ontology/modules/biobank-specimens.owl +++ b/src/ontology/modules/biobank-specimens.owl @@ -166,7 +166,7 @@ - A specimen that is derived from amniotic fluid. + A specimen that is derived from amniotic fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank amniotic fluid specimen @@ -206,7 +206,7 @@ - A specimen that is derived from bile. + A specimen that is derived from bile. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bile specimen @@ -246,7 +246,7 @@ - A specimen that is derived from cerbrospinal fluid. + A specimen that is derived from cerbrospinal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen @@ -286,7 +286,7 @@ - A specimen that is derived from feces. + A specimen that is derived from feces. Chris Stoeckert stool specimen Chris Stoeckert, Penn Medicine Biobank @@ -327,7 +327,7 @@ - A specimen that is derived from digestive system fluid or secretion. + A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert gastric fluid specimen Chris Stoeckert, Penn Medicine Biobank @@ -368,7 +368,7 @@ - A specimen that is derived from milk. + A specimen that is derived from milk. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank milk specimen @@ -408,7 +408,7 @@ - A specimen that is derived from pericardial fluid. + A specimen that is derived from pericardial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pericardial fluid specimen @@ -448,7 +448,7 @@ - A specimen that is derived from saliva. + A specimen that is derived from saliva. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank saliva specimen @@ -488,7 +488,7 @@ - A specimen that is derived from sputum. + A specimen that is derived from sputum. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sputum specimen @@ -528,7 +528,7 @@ - A specimen that is derived from sweat. + A specimen that is derived from sweat. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sweat specimen @@ -568,7 +568,7 @@ - A specimen that is derived from synovial fluid. + A specimen that is derived from synovial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank synovial fluid specimen @@ -618,7 +618,7 @@ - A specimen that is derived from vireous humor. + A specimen that is derived from vireous humor. Chris Stoeckert vitreous fluid specimen Chris Stoeckert, Penn Medicine Biobank @@ -659,7 +659,7 @@ - A specimen that is derived from bone marrow. + A specimen that is derived from bone marrow. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bone marrow specimen @@ -709,7 +709,7 @@ - A specimen that is derived from placenta. + A specimen that is derived from placenta. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank placenta specimen @@ -749,7 +749,7 @@ - A specimen that is derived from peritoneal fluid. + A specimen that is derived from peritoneal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank peritoneal fluid specimen @@ -789,7 +789,7 @@ - A specimen that is derived from pleural fluid. + A specimen that is derived from pleural fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen @@ -839,7 +839,7 @@ - A specimen that is derived from brain. + A specimen that is derived from brain. Chris Stoeckert Chris Stoeckert, NCI BBRB brain specimen @@ -879,7 +879,7 @@ - A specimen that is derived from hair. + A specimen that is derived from hair. Chris Stoeckert Chris Stoeckert, NCI BBRB hair specimen @@ -929,7 +929,7 @@ - A specimen that is derived from prostate gland. + A specimen that is derived from prostate gland. Chris Stoeckert Chris Stoeckert, NCI BBRB prostate gland specimen @@ -969,7 +969,7 @@ - A specimen that is derived from skeletal muscle. + A specimen that is derived from skeletal muscle. Chris Stoeckert Chris Stoeckert, NCI BBRB skeletal muscle tissue specimen @@ -1019,7 +1019,7 @@ - A specimen that is derived from heart. + A specimen that is derived from heart. Chris Stoeckert Chris Stoeckert, NCI BBRB heart specimen @@ -1069,7 +1069,7 @@ - A specimen that is derived from renal medulla. + A specimen that is derived from renal medulla. Chris Stoeckert kidney medulla specimen Chris Stoeckert, NCI BBRB @@ -1120,7 +1120,7 @@ - A specimen that is derived from adrenal gland. + A specimen that is derived from adrenal gland. Chris Stoeckert Chris Stoeckert, NCI BBRB adrenal gland specimen @@ -1170,7 +1170,7 @@ - A specimen that is derived from breast. + A specimen that is derived from breast. Chris Stoeckert mammary tissue specimen Chris Stoeckert, NCI BBRB @@ -1221,7 +1221,7 @@ - A specimen that is derived from urinary bladder. + A specimen that is derived from urinary bladder. Chris Stoeckert Chris Stoeckert, NCI BBRB urinary bladder specimen @@ -1271,7 +1271,7 @@ - A specimen that is derived from tibial artery. + A specimen that is derived from tibial artery. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial artery specimen @@ -1321,7 +1321,7 @@ - A specimen that is derived from skin. + A specimen that is derived from skin. Chris Stoeckert skin specimen Chris Stoeckert, NCI BBRB @@ -1372,7 +1372,7 @@ - A specimen that is derived from pancreas. + A specimen that is derived from pancreas. Chris Stoeckert Chris Stoeckert, NCI BBRB pancreas specimen @@ -1422,7 +1422,7 @@ - A specimen that is derived from stomach. + A specimen that is derived from stomach. Chris Stoeckert Chris Stoeckert, NCI BBRB stomach specimen @@ -1472,7 +1472,7 @@ - A specimen that is derived from pituitary gland. + A specimen that is derived from pituitary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB pituitary gland specimen @@ -1512,7 +1512,7 @@ - A specimen that is derived from adipose tissue. + A specimen that is derived from adipose tissue. Chris Stoeckert Chris Stoeckert, NCI BBRB adipose tissue specimen @@ -1562,7 +1562,7 @@ - A specimen that is derived from cortex of kidney. + A specimen that is derived from cortex of kidney. Chris Stoeckert kidney cortex specimen Chris Stoeckert, NCI BBRB @@ -1613,7 +1613,7 @@ - A specimen that is derived from esophagus mucosa. + A specimen that is derived from esophagus mucosa. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagus mucosa specimen @@ -1663,7 +1663,7 @@ - A specimen that is derived from colon. + A specimen that is derived from colon. Chris Stoeckert Chris Stoeckert, NCI BBRB colon specimen @@ -1713,7 +1713,7 @@ - A specimen that is derived from lung. + A specimen that is derived from lung. Chris Stoeckert Chris Stoeckert, NCI BBRB lung specimen @@ -1763,7 +1763,7 @@ - A specimen that is derived from esophagus muscularis mucosa. + A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert esophagus muscularis specimen Chris Stoeckert, NCI BBRB @@ -1814,7 +1814,7 @@ - A specimen that is derived from cerebral cortex. + A specimen that is derived from cerebral cortex. Chris Stoeckert brain cortex specimen Chris Stoeckert, NCI BBRB @@ -1865,7 +1865,7 @@ - A specimen that is derived from thyroid gland. + A specimen that is derived from thyroid gland. Chris Stoeckert Chris Stoeckert, NCI BBRB thyroid gland specimen @@ -1915,7 +1915,7 @@ - A specimen that is derived from cerebellum. + A specimen that is derived from cerebellum. Chris Stoeckert brain cerebellum specimen Chris Stoeckert, NCI BBRB @@ -1966,7 +1966,7 @@ - A specimen that is derived from tibial nerve. + A specimen that is derived from tibial nerve. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial nerve specimen @@ -2016,7 +2016,7 @@ - A specimen that is derived from coronary artery. + A specimen that is derived from coronary artery. Chris Stoeckert Chris Stoeckert, NCI BBRB coronary artery specimen @@ -2066,7 +2066,7 @@ - A specimen that is derived from spleen. + A specimen that is derived from spleen. Chris Stoeckert Chris Stoeckert, NCI BBRB spleen specimen @@ -2116,7 +2116,7 @@ - A specimen that is derived from aorta. + A specimen that is derived from aorta. Chris Stoeckert Chris Stoeckert, NCI BBRB aorta specimen @@ -2166,7 +2166,7 @@ - A specimen that is derived from the atrium auricular region. + A specimen that is derived from the atrium auricular region. Chris Stoeckert Chris Stoeckert, NCI BBRB atrial appendage specimen @@ -2216,7 +2216,7 @@ - A specimen that is derived from the esophagogastric junction. + A specimen that is derived from the esophagogastric junction. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagogastric junction specimen @@ -2266,7 +2266,7 @@ - A specimen that is derived from ileum. + A specimen that is derived from ileum. Chris Stoeckert Chris Stoeckert, NCI BBRB ileum specimen @@ -2316,7 +2316,7 @@ - A specimen that is derived from liver. + A specimen that is derived from liver. Chris Stoeckert Chris Stoeckert, NCI BBRB liver specimen @@ -2366,7 +2366,7 @@ - A specimen that is derived from minor salivary gland. + A specimen that is derived from minor salivary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB minor salivary gland specimen @@ -2416,7 +2416,7 @@ - A specimen that is derived from omentum. + A specimen that is derived from omentum. Chris Stoeckert Chris Stoeckert, NCI BBRB omentum specimen @@ -2466,7 +2466,7 @@ - A specimen that is derived from female gonad. + A specimen that is derived from female gonad. Chris Stoeckert Chris Stoeckert, NCI BBRB ovary specimen @@ -2516,7 +2516,7 @@ - A specimen that is derived from sigmoid colon. + A specimen that is derived from sigmoid colon. Chris Stoeckert Chris Stoeckert, NCI BBRB sigmoid colon specimen @@ -2566,7 +2566,7 @@ - A specimen that is derived from suprapubic skin. + A specimen that is derived from suprapubic skin. Chris Stoeckert Chris Stoeckert, NCI BBRB suprapubic skin specimen @@ -2616,7 +2616,7 @@ - A specimen that is derived from testis. + A specimen that is derived from testis. Chris Stoeckert Chris Stoeckert, NCI BBRB testis specimen @@ -2666,7 +2666,7 @@ - A specimen that is derived from uterus. + A specimen that is derived from uterus. Chris Stoeckert Chris Stoeckert, NCI BBRB uterus specimen @@ -2716,7 +2716,7 @@ - A specimen that is derived from vagina. + A specimen that is derived from vagina. Chris Stoeckert Chris Stoeckert, NCI BBRB vagina specimen @@ -2768,7 +2768,7 @@ - A specimen that is collected with a swab from the surface of an areola of a breast. + 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 @@ -2814,7 +2814,7 @@ - A specimen that is collected with a swab from the surface of a breast. + A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert Chris Stoeckert, OBIB breast swab specimen @@ -2860,7 +2860,7 @@ - A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. + 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 @@ -2906,7 +2906,7 @@ - A specimen that is collected with a swab from the surface of a nasopharynx. + A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert Chris Stoeckert, OBIB nasopharyngeal swab specimen @@ -2952,7 +2952,7 @@ - A specimen that is collected with a swab from the inside surface of a mouth. + A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert Chris Stoeckert, OBIB oral swab specimen @@ -2998,7 +2998,7 @@ - A specimen that is collected with a swab from the surface of a oropharynx. + A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert Chris Stoeckert, OBIB oropharyngeal swab specimen @@ -3044,7 +3044,7 @@ - A specimen that is collected with a swab from the surface of a rectum. + A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert Chris Stoeckert, OBIB rectal swab specimen @@ -3090,7 +3090,7 @@ - A specimen that is collected with a swab from the surface of a tongue. + A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert Chris Stoeckert, OBIB tongue swab specimen @@ -3136,7 +3136,7 @@ - A specimen that is collected with a swab from the surface of a vagina. + A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert Chris Stoeckert, OBIB vagina swab specimen @@ -3182,7 +3182,7 @@ - A specimen that is collected with a swab from the surface of a feces. + A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert stool swab specimen Chris Stoeckert, OBIB @@ -3229,7 +3229,7 @@ - A specimen that is collected with a swab from the surface of an environmenal material. + A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert Chris Stoeckert, OBIB environmental swab specimen @@ -3272,7 +3272,7 @@ - A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. + A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. John Judkins PMC3297553 induced sputum specimen @@ -3315,7 +3315,7 @@ - A specimen that is collected with a suctioning tube from the trachea. + 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 @@ -3361,7 +3361,7 @@ - A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. + 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 @@ -3406,7 +3406,7 @@ - A specimen that is collected with a suctioning tube from the nasal cavity. + 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 @@ -3453,7 +3453,7 @@ - A specimen that is collected with a suctioning tube from the lower respiratory tract. + 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 @@ -3499,7 +3499,7 @@ - A specimen that is derived from the upper respiratory tract + 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 @@ -3531,7 +3531,7 @@ - A specimen that is derived from the lower respiratory tract. + 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 @@ -3576,7 +3576,7 @@ - A specimen that is derived from the anterior nasal wall + 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 @@ -3619,7 +3619,7 @@ - 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. + 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 @@ -3656,7 +3656,7 @@ - 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. + 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 @@ -3693,7 +3693,7 @@ - A blood specimen that is located in a vacutainer. + A blood specimen that is located in a vacutainer. John Judkins Vacutainer sample VEuPathDB @@ -3731,7 +3731,7 @@ - A blood specimen that is located on a filter paper. + A blood specimen that is located on a filter paper. Chris Stoeckert Jie Zheng Filter paper sample @@ -3772,7 +3772,7 @@ - A specimen that is derived from placental blood. + A specimen that is derived from placental blood. John Judkins VEuPathDB placental blood specimen @@ -3809,7 +3809,7 @@ - A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. + A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. Chris Stoeckert Jie Zheng PBMC specimen @@ -3858,7 +3858,7 @@ - A specimen that is derived from a portion of lymph collected from an organism. + A specimen that is derived from a portion of lymph collected from an organism. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB lymph specimen @@ -3905,7 +3905,7 @@ - A specimen that is derived from part of a digestive tract. + A specimen that is derived from part of a digestive tract. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB digestive tract specimen @@ -3948,7 +3948,7 @@ - A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. + A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Randi Vita Sebastian Duesing nasal lavage fluid @@ -4009,7 +4009,7 @@ - A specimen that is derived from some uterine cervix + 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 @@ -4060,7 +4060,7 @@ - A specimen that is derived from some urethra + 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 @@ -4101,7 +4101,7 @@ - A specimen that is derived from some cervical mucus + 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 @@ -4152,7 +4152,7 @@ - A specimen that is derived from some throat + 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 @@ -4203,7 +4203,7 @@ - A specimen that is derived from some eye + 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 @@ -4254,7 +4254,7 @@ - A specimen that is derived from some respiratory system + 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 @@ -4305,7 +4305,7 @@ - A specimen that is derived from some upper respiratory tract + 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 @@ -4356,7 +4356,7 @@ - A specimen that is derived from some nasopharynx + 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 @@ -4397,7 +4397,7 @@ - A specimen that is derived from some semen + 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 @@ -4438,7 +4438,7 @@ - A specimen that is derived from some bodily fluid + 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 @@ -4489,7 +4489,7 @@ - A specimen that is derived from some chorionic villus + 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 @@ -4530,7 +4530,7 @@ - A specimen that is derived from some meconium + 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 @@ -4571,7 +4571,7 @@ - A specimen that is derived from some umbilical cord blood + 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 @@ -4612,7 +4612,7 @@ - A specimen that is derived from some arterial blood + 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 @@ -4653,7 +4653,7 @@ - A specimen that is derived from some venous blood + 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 @@ -4694,7 +4694,7 @@ - A specimen that is derived from some capillary blood + 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 @@ -4739,7 +4739,7 @@ - A specimen that is derived from some erythrocytes + 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 @@ -4784,7 +4784,7 @@ - A specimen that is derived from some reticulocytes + 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 @@ -4829,7 +4829,7 @@ - A specimen that is derived from some leukocytes + 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 diff --git a/src/ontology/modules/biopsy.owl b/src/ontology/modules/biopsy.owl index 43cf512c..48c01296 100644 --- a/src/ontology/modules/biopsy.owl +++ b/src/ontology/modules/biopsy.owl @@ -146,7 +146,7 @@ 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. + 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 @@ -161,7 +161,7 @@ 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. + A biopsy which uses an imaging procedure to guide a needle biopsy. Damion Dooley image guided needle biopsy image-guided biopsy @@ -184,7 +184,7 @@ 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. + A needle biopsy guided by real-time computed tomography (CT) scan images. Damion Dooley CT Assisted Biopsy CT Guided Biopsy @@ -202,7 +202,7 @@ 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. + 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 @@ -222,7 +222,7 @@ 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. + 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 @@ -236,7 +236,7 @@ A fine needle aspiration biopsy is commonly performed in order to test for cancer. - A biopsy that uses a thin needle to extract cells. + A biopsy that uses a thin needle to extract cells. Chris Stoeckert, Helena Ellis, Jie Zheng FNA FNAB @@ -253,7 +253,7 @@ 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. + 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/ @@ -269,7 +269,7 @@ 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. + A biopsy involving a surgical incision into an organism to access the biopsy material. Damion Dooley excisional biopsy open biopsy @@ -291,7 +291,7 @@ 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. + A biopsy involving the collection of a small part of the abdominal wall fat pad. Nicole Vasilevsky, Damion Dooley abdominal wall biopsy fat biopsy @@ -313,7 +313,7 @@ A mouse tail biopsy was performed to collect material for DNA extraction. - A biopsy involving the collection of the tip of a mamallian tail. + 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 @@ -334,7 +334,7 @@ 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. + 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 @@ -354,7 +354,7 @@ 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. + 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 @@ -381,7 +381,7 @@ 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. + A biopsy performed with a needle augmented with a vacuum device. Damion Dooley VAB https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ diff --git a/src/ontology/modules/data-sets.owl b/src/ontology/modules/data-sets.owl index f553bb20..cab821ed 100644 --- a/src/ontology/modules/data-sets.owl +++ b/src/ontology/modules/data-sets.owl @@ -121,13 +121,13 @@ The output produced by a digital imaging technique, such as microscopy, MRI, or CT. - A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set @@ -149,13 +149,13 @@ The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan. - An image data set whose information content originates from some MR imaging assay and is about some MRI participant. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + An image data set whose information content originates from some MR imaging assay and is about some MRI participant. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" MRI at a Glance, ISBN 10: 1119053552 https://github.com/obi-ontology/obi/issues/1481 magnetic resonance image data set @@ -173,15 +173,15 @@ - The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. - An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. + An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw image data set @@ -203,13 +203,13 @@ The production of JPEG file by a digital camera. - An image data set that is the output of an image data set analysis. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + An image data set that is the output of an image data set analysis. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 computed image data set @@ -230,14 +230,14 @@ - The product of a mathematical transformation of raw "k-space" data produced by an MRI machine into a form that represents the anatomical structure of the brain. - An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + The product of a mathematical transformation of raw "k-space" data produced by an MRI machine into a form that represents the anatomical structure of the brain. + An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 reconstructed magnetic resonance image data set @@ -249,9 +249,9 @@ MRI used for assessing structural integrity of brain axons and visualizing ischemia. - A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor "b," which is a function of the amplitude, duration, and interval of the gradiants. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor "b," which is a function of the amplitude, duration, and interval of the gradiants. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 diffusion weighted magnetic resonance image data set @@ -263,11 +263,11 @@ MRI used for assessing brain activity via blood oxygen level dependent signal. - An magnetic resonance image data set collected as a 4D time series representing changes in brain metabolism (i.e. BOLD), typically used as a proxy for brain activity. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + An magnetic resonance image data set collected as a 4D time series representing changes in brain metabolism (i.e. BOLD), typically used as a proxy for brain activity. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 functional magnetic resonance image data set @@ -279,10 +279,10 @@ An fMRI used for assessing functional connectivity of brain regions at rest. - A type of functional MRI in which the participant is not given a task, but just rests during acquisision - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A type of functional MRI in which the participant is not given a task, but just rests during acquisision + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 resting state functional magnetic resonance image data set @@ -294,10 +294,10 @@ fMRI type used for assessing brain activity while performing an action or in response to stimuli. - A type of functional MRI in which the participant is given a task or tasks, which are timed with the acquisition - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A type of functional MRI in which the participant is given a task or tasks, which are timed with the acquisition + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 task-based functional magnetic resonance image data set @@ -309,9 +309,9 @@ MRI used for evaluating ischemia. - An magnetic resonance image data set that captures volume and flow of blood in the brain. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + An magnetic resonance image data set that captures volume and flow of blood in the brain. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 perfusion weighted magnetic resonance image data set @@ -323,10 +323,10 @@ MRI used for visualizing structure of tissue. - An magnetic resonance image data set in which the contrast emphasizes density of protons, supressing T1 and T2 effects - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + An magnetic resonance image data set in which the contrast emphasizes density of protons, supressing T1 and T2 effects + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 proton density magnetic resonance image data set @@ -338,10 +338,10 @@ MRI used for visualizing structure of tissue where fluid is hypointense. - An magnetic resonance image acquired using a T1 weighted magnetic resonance image acquisition sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + An magnetic resonance image acquired using a T1 weighted magnetic resonance image acquisition sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T1 weighted magnetic resonance image data set @@ -353,10 +353,10 @@ MRI used for assessing breakdown of blood brain barrier. - A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquistion. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquistion. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 post-Gd T1 weighted magnetic resonance image data set @@ -368,10 +368,10 @@ MRI used for computational research on the structure of tissue. - T1 weighted image data set collected using a gradient recall echo sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + T1 weighted image data set collected using a gradient recall echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T1 weighted GRE magnetic resonance image data set @@ -383,10 +383,10 @@ MRI used for computational segmentation of tissue due to high quality. - A T1-weighted image data set acquired from an NMR/MRI machine with at least a 3 Tesla magnet and in which the voxel size is isotropic. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A T1-weighted image data set acquired from an NMR/MRI machine with at least a 3 Tesla magnet and in which the voxel size is isotropic. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 high resolution T1 weighted magnetic resonance image data set @@ -398,10 +398,10 @@ First MRI acquired as part of longitudinal study. - A T1w image data set collected at an evaluant's first visit in a study. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A T1w image data set collected at an evaluant's first visit in a study. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 baseline high resolution T1 weighted magnetic resonance image data set @@ -413,10 +413,10 @@ MRI acquired after the first scan as part of longitudinal study. - A T1w image data set collected at a later time than the evaluant's first scan. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A T1w image data set collected at a later time than the evaluant's first scan. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 follow-up high resolution T1 weighted magnetic resonance image data set @@ -428,10 +428,10 @@ MRI used for visualizing structure of tissue, often of lower quality than a GRE sequence. - A T1 weighted image data set acquired using a spin echo sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A T1 weighted image data set acquired using a spin echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T1 weighted SE magnetic resonance image data set @@ -443,10 +443,10 @@ MRI used for visualizing structure of tissue where fluid is hyperintense. - A magnetic resonance image produced by a T2 weighted magnetic resonance image acquisition sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A magnetic resonance image produced by a T2 weighted magnetic resonance image acquisition sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2 weighted magnetic resonance image data set @@ -458,10 +458,10 @@ MRI used for visualizing lesions in multiple sclerosis. - A T2 weighted image data set collected using a FLAIR sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A T2 weighted image data set collected using a FLAIR sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2 weighted FLAIR magnetic resonance image data set @@ -473,10 +473,10 @@ MRI used for visualizing structure of tissue with fast acquisition times. - T2 weighted image collected using a fast/turbo spin echo sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + T2 weighted image collected using a fast/turbo spin echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" T2 weighted TSE magnetic resonance image data set https://github.com/obi-ontology/obi/issues/1481 T2 weighted FSE magnetic resonance image data set @@ -489,10 +489,10 @@ MRI used for visualizing structure of tissue, often longer acquisition than FSE sequence. - A type of T2-weighted image in which the acquisition is performed using a 2D spin-echo technique - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + A type of T2-weighted image in which the acquisition is performed using a 2D spin-echo technique + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2 weighted SE magnetic resonance image data set @@ -504,9 +504,9 @@ MRI used for visualizing structure of tissue where signal from fat is suppressed. - A T2 weighted magnetic resonance image data set collected using a STIR sequence to suppress the signal coming from fat. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + A T2 weighted magnetic resonance image data set collected using a STIR sequence to suppress the signal coming from fat. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 T2 weighted STIR magnetic resonance image data set @@ -518,10 +518,10 @@ MRI better suited for identifying focal pathology than T2w SE sequences. - T2* weighted image data set collected using a gradient echo sequence. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + T2* weighted image data set collected using a gradient echo sequence. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2* weighted GRE magnetic resonance image data set @@ -546,10 +546,10 @@ - The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. - An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. + An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set @@ -573,12 +573,12 @@ The Desikan-Killiany brain region atlas used by the FreeSurfer software suite. - An image data set consisting of values computed from multiple image data sets encoded to represent the spatial location of individual functional or structural regions of a canonical brain. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + An image data set consisting of values computed from multiple image data sets encoded to represent the spatial location of individual functional or structural regions of a canonical brain. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 brain region atlas image data set @@ -590,10 +590,10 @@ A brain atlas of resting-state functional networks derived from the probability that disparate brains regions are active at the same time. - A brain atlas consisting of weighted values that respresent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + A brain atlas consisting of weighted values that respresent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 probabilistic brain region atlas image dataset @@ -605,10 +605,10 @@ The JHU white-matter tractography atlas used for mapping brain connectomes. - A brain atlas consisting of discrete integer values where a value X denotes a voxel is part of some brain component Y. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + A brain atlas consisting of discrete integer values where a value X denotes a voxel is part of some brain component Y. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 deterministic brain region atlas image data set @@ -620,12 +620,12 @@ The output of an algorithm that identifies pedestrians walking in a street from an image data set, where the output contains values only in the segment where the pedestrian is present. - An image data set of integer values in which each value corresponds to some shared characteristic or computed property. The values often belong to a group of pixels or voxels that share the same characteristic, such as a tissue type or anatomical region. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + An image data set of integer values in which each value corresponds to some shared characteristic or computed property. The values often belong to a group of pixels or voxels that share the same characteristic, such as a tissue type or anatomical region. + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image segmentation map @@ -637,9 +637,9 @@ The output produced by a manual or automated segmentation of lesions from a brain MRI. - An image data set where voxel intensity values greater than zero encode the location of some brain lesion and voxels outside the lesion have an intensity value of zero. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + An image data set where voxel intensity values greater than zero encode the location of some brain lesion and voxels outside the lesion have an intensity value of zero. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 lesion mask @@ -651,9 +651,9 @@ The output produced by a manual or automated segmentation of lesions from a T1w MRI. - A lesion mask where the lesions are derived from a T1 weighted image data set. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + A lesion mask where the lesions are derived from a T1 weighted image data set. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 T1 lesion mask @@ -665,9 +665,9 @@ The output produced by a manual or automated segmentation of lesions from a T2w FLAIR MRI. - A lesion mask where the lesions are derived from a T2 FLAIR image data set. - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + A lesion mask where the lesions are derived from a T2 FLAIR image data set. + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 T2 FLAIR lesion mask diff --git a/src/ontology/modules/data-transformations.owl b/src/ontology/modules/data-transformations.owl index 682dd8da..919f15f2 100644 --- a/src/ontology/modules/data-transformations.owl +++ b/src/ontology/modules/data-transformations.owl @@ -144,7 +144,7 @@ - The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. + The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" @@ -176,7 +176,7 @@ A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. - A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. + A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index 4e31ff82..745ec45a 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -228,7 +228,7 @@ 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. + 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 @@ -249,7 +249,7 @@ pump valve switch - A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. + 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 @@ -288,7 +288,7 @@ 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. + 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 @@ -329,7 +329,7 @@ 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 + 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 @@ -367,7 +367,7 @@ 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. + 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 @@ -393,7 +393,7 @@ microarray platform - A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. + 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 @@ -414,7 +414,7 @@ gamma counter A Geiger counter - A processed material which measures gamma radiation + A processed material which measures gamma radiation Frank Gibson http://en.wikipedia.org/wiki/Gamma_counter gamma counter @@ -435,7 +435,7 @@ polystyrene tube Polystyrene tubes can be used to contain tissue culture cells during centrifgation - A polystyrene tube is a test tube made of polystyrene + A polystyrene tube is a test tube made of polystyrene PERSON: Chris Stoeckert PERSON: Chris Stoeckert polystyrene tube @@ -456,7 +456,7 @@ 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 + 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 @@ -476,7 +476,7 @@ 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. + 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 @@ -496,7 +496,7 @@ filter paper - A device manufacture with the intent to provide a porous unsized paper used for filtering. + A device manufacture with the intent to provide a porous unsized paper used for filtering. Frank Gibson sep:00107 filter paper @@ -517,7 +517,7 @@ 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. + 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 @@ -545,7 +545,7 @@ 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. + 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 @@ -567,7 +567,7 @@ 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))). + 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 @@ -588,7 +588,7 @@ 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. + 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 @@ -716,7 +716,7 @@ 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. + 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 @@ -743,7 +743,7 @@ 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 + 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 @@ -775,7 +775,7 @@ blot module - A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised + 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 @@ -811,7 +811,7 @@ image acquisition device - An image creation device is a device which captures a digitized image of an object + An image creation device is a device which captures a digitized image of an object Frank Gibson image acquisition device sep:00096 @@ -856,7 +856,7 @@ 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 + 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 @@ -883,7 +883,7 @@ 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 + 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 @@ -904,7 +904,7 @@ 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. + 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 @@ -918,7 +918,7 @@ 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. + 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 @@ -945,7 +945,7 @@ 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. + 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 @@ -961,7 +961,7 @@ Bruker autosampler - A Bruker autosampler is an autosampler made by Bruker. + 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 @@ -976,7 +976,7 @@ 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. + 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 @@ -991,7 +991,7 @@ 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). + 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> @@ -1007,7 +1007,7 @@ 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. + 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 @@ -1023,7 +1023,7 @@ 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. + 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 @@ -1039,7 +1039,7 @@ 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. + 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 @@ -1054,7 +1054,7 @@ 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. + 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 @@ -1070,7 +1070,7 @@ nano pump system - A pump system optimized for nano flow chromatography. + 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 @@ -1085,7 +1085,7 @@ 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. + 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> @@ -1101,7 +1101,7 @@ manual injection system - The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. + 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 @@ -1116,7 +1116,7 @@ Varian GEMINI spectrometer - An older Varian Broadband NMR 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 @@ -1132,7 +1132,7 @@ 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. + 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 @@ -1148,7 +1148,7 @@ solid NMR probe - An NMR probe that is designed to hold a solid sample. + 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 @@ -1164,7 +1164,7 @@ 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. + 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> @@ -1181,7 +1181,7 @@ 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. + 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 @@ -1196,7 +1196,7 @@ 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. + 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 @@ -1211,7 +1211,7 @@ 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. + 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 @@ -1227,7 +1227,7 @@ 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. + 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 @@ -1249,7 +1249,7 @@ chromatography instrument - Any instrument that is used to carry out a chromatography experiment. + 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 @@ -1265,7 +1265,7 @@ 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). + 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 @@ -1281,7 +1281,7 @@ 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. + 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 @@ -1297,7 +1297,7 @@ 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. + 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 @@ -1312,7 +1312,7 @@ cation exchange column - A cation exchange column is a chromatography column that is used in cation exchange chromatography. + 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 @@ -1327,7 +1327,7 @@ direct detection NMR probe - An NMR probe designed to allow the direct detection of acquisition nuclei. + 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 @@ -1343,7 +1343,7 @@ 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. + 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 @@ -1365,7 +1365,7 @@ 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. + 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 @@ -1380,7 +1380,7 @@ liquid chromatography autosampler - Designed to perform capillary LC with injection of sample volumes ranging from nL to L. + 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 @@ -1395,7 +1395,7 @@ 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. + 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 @@ -1410,7 +1410,7 @@ capillary column - A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. + 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 @@ -1425,7 +1425,7 @@ 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. + 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 @@ -1441,7 +1441,7 @@ 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. + 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 @@ -1457,7 +1457,7 @@ NMR console - A component of an NMR instrument that controls the activities of the other components. + 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 @@ -1473,7 +1473,7 @@ 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). + 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 @@ -1494,7 +1494,7 @@ variable wavelength detector - A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. + 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 @@ -1509,7 +1509,7 @@ 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. + 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 @@ -1526,7 +1526,7 @@ 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. + 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 @@ -1548,7 +1548,7 @@ multiple wavelength detector - A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. + 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 @@ -1563,7 +1563,7 @@ 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. + 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> @@ -1579,7 +1579,7 @@ 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. + 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 @@ -1595,7 +1595,7 @@ 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. + 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 @@ -1611,7 +1611,7 @@ 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. + 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> @@ -1627,7 +1627,7 @@ 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. + 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 @@ -1642,7 +1642,7 @@ injector lubricant - A lubricant used in liquid chromatography that eases sample injector penetration. + 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 @@ -1657,7 +1657,7 @@ 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. + 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 @@ -1673,7 +1673,7 @@ 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. + 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 @@ -1689,7 +1689,7 @@ 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. + 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 @@ -1716,7 +1716,7 @@ 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. + 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 @@ -1732,7 +1732,7 @@ 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. + 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 @@ -1748,7 +1748,7 @@ 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. + 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 @@ -1763,7 +1763,7 @@ 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. + 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 @@ -1779,7 +1779,7 @@ 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. + 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> @@ -1795,7 +1795,7 @@ vial - A container made from solid material and primarily used for holding liquid. + 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 @@ -1815,7 +1815,7 @@ 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. + 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> @@ -1832,7 +1832,7 @@ Varian VXR spectrometer - A Varian NMR 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 @@ -1848,7 +1848,7 @@ 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. + 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 @@ -1863,7 +1863,7 @@ preparative autosampler - For preparative LC with injection of sample volumes ranging from L to mL ranges. + 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 @@ -1878,7 +1878,7 @@ 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. + 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> @@ -1895,7 +1895,7 @@ 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. + 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 @@ -1911,7 +1911,7 @@ JEOL NMR probe - An NMR probe that is manufactured by JEOL. + 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 @@ -1927,7 +1927,7 @@ 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. + 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 @@ -1943,7 +1943,7 @@ 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. + 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 @@ -1959,7 +1959,7 @@ 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. + 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 @@ -1974,7 +1974,7 @@ 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. + 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 @@ -1989,7 +1989,7 @@ tecmag NMR instrument - An NMR instrument that is manufactured by tecmag. + 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 @@ -2005,7 +2005,7 @@ 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. + 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 @@ -2020,7 +2020,7 @@ 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. + 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 @@ -2035,7 +2035,7 @@ 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. + 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 @@ -2050,7 +2050,7 @@ imaging NMR probe - An NMR probe that is designed for generating pictures from sample states via NMR imaging. + 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 @@ -2066,7 +2066,7 @@ Bruker AC series NMR instrument - A series of older Bruker NMR magnets, now out of production. + 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 @@ -2082,7 +2082,7 @@ gas chromatography equipment - Any device used in a gas chromatography experiment. + 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 @@ -2098,7 +2098,7 @@ syringe filter - A small membrane filter of defined pore size, that filters samples from a syringe. + 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 @@ -2119,7 +2119,7 @@ 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. + 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 @@ -2135,7 +2135,7 @@ 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. + 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 @@ -2150,7 +2150,7 @@ capillary pump system - A pump system optimized for capillary chromatography. + 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 @@ -2171,7 +2171,7 @@ 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. + 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 @@ -2186,7 +2186,7 @@ column cartridger - A chromatography device where the column cartridge is inserted into and stabilised. + 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 @@ -2201,7 +2201,7 @@ nitrogen generator - A gas generator that generates nitrogen gas. + 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 @@ -2216,7 +2216,7 @@ needle assembly - The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet + 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 @@ -2231,7 +2231,7 @@ 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. + 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 @@ -2248,7 +2248,7 @@ 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. + 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 @@ -2264,7 +2264,7 @@ 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. + 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 @@ -2280,7 +2280,7 @@ isocratic pump system - A pump system optimized for isocratic chromatography. + 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 @@ -2295,7 +2295,7 @@ 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). + 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 @@ -2310,7 +2310,7 @@ 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. + 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 @@ -2326,7 +2326,7 @@ liquid NMR probe - An NMR probe that is designed to hold a liquid sample. + 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 @@ -2342,7 +2342,7 @@ 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. + 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 @@ -2357,7 +2357,7 @@ Bruker NMR probe - An NMR probe that is manufactured by Bruker. + 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 @@ -2373,7 +2373,7 @@ anion trap column - An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. + 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 @@ -2394,7 +2394,7 @@ 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. + 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 @@ -2409,7 +2409,7 @@ 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. + 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 @@ -2431,7 +2431,7 @@ 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. + 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 @@ -2452,7 +2452,7 @@ NMR instrument - An Instrument which is used to carry out a NMR analysis of some sample. + An Instrument which is used to carry out a NMR analysis of some sample. PERSON:Daniel Schober MRI scanner NMR instrument @@ -2471,7 +2471,7 @@ 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. + 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 @@ -2487,7 +2487,7 @@ 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. + 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 @@ -2502,7 +2502,7 @@ 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. + 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> @@ -2518,7 +2518,7 @@ 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. + 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 @@ -2533,7 +2533,7 @@ 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. + 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 @@ -2549,7 +2549,7 @@ gradient pump system - A pump system optimized for gradient chromatography. + 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 @@ -2564,7 +2564,7 @@ high temperature column - A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. + 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 @@ -2579,7 +2579,7 @@ 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. + 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 @@ -2601,7 +2601,7 @@ 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. + 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 @@ -2617,7 +2617,7 @@ Varian UNITY spectrometer - The predecessor series of the Varian UNITY INOVA 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 @@ -2633,7 +2633,7 @@ 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. + 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 @@ -2649,7 +2649,7 @@ 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. + 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 @@ -2664,7 +2664,7 @@ Bruker LC-NMR/MS platform - Includes the connection to a high-resolution TOF-LC-MS system. + 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 @@ -2687,7 +2687,7 @@ 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. + 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 @@ -2702,7 +2702,7 @@ 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. + 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 @@ -2717,7 +2717,7 @@ 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. + 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 @@ -2732,7 +2732,7 @@ 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. + 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> @@ -2748,7 +2748,7 @@ 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). + 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 @@ -2763,7 +2763,7 @@ 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. + 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 @@ -2779,7 +2779,7 @@ 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. + 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> @@ -2796,7 +2796,7 @@ chromatography detector filter - An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. + 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 @@ -2811,7 +2811,7 @@ cation trap column - A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. + 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 @@ -2826,7 +2826,7 @@ column adapter - An Adapter that enabled the connection of a column to additional devices. + 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 @@ -2848,7 +2848,7 @@ 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). + 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> @@ -2864,7 +2864,7 @@ Bruker NMR instrument - An NMR instrument that is manufactured by Bruker. + 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 @@ -2880,7 +2880,7 @@ Bruker NMR magnet - An NMR magnet that is manufactured by Bruker. + 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 @@ -2896,7 +2896,7 @@ 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. + 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 @@ -2911,7 +2911,7 @@ tecmag NMR console - An NMR console manufactured by tecmac. + 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 @@ -2927,7 +2927,7 @@ JEOL NMR instrument - An NMR instrument that is manufactured by JEOL. + 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 @@ -2943,7 +2943,7 @@ chromatography consumable - A chromatography consumable is a consumable that is used in a chromatography experiment. + 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 @@ -2959,7 +2959,7 @@ 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). + 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 @@ -2975,7 +2975,7 @@ 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. + 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 @@ -2990,7 +2990,7 @@ 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. + 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 @@ -3005,7 +3005,7 @@ 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. + 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 @@ -3021,7 +3021,7 @@ 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. + 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 @@ -3036,7 +3036,7 @@ 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. + 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> @@ -3053,7 +3053,7 @@ hydrogen generator - A gas generator that generates hydrogen gas. + 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 @@ -3068,7 +3068,7 @@ 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. + 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 @@ -3083,7 +3083,7 @@ auto injector - A gas chromatography device that can auto-inject a small number of samples an inlet. + 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 @@ -3098,7 +3098,7 @@ Varian NMR instrument - An NMR instrument that is manufactured by Varian. + 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 @@ -3114,7 +3114,7 @@ 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. + 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> @@ -3131,7 +3131,7 @@ 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. + 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 @@ -3148,7 +3148,7 @@ 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. + 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 @@ -3164,7 +3164,7 @@ 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. + 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> @@ -3181,7 +3181,7 @@ 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. + 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 @@ -3196,7 +3196,7 @@ 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. + 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 @@ -3211,7 +3211,7 @@ 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. + 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 @@ -3227,7 +3227,7 @@ 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. + 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 @@ -3243,7 +3243,7 @@ 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. + 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 @@ -3258,7 +3258,7 @@ 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. + 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 @@ -3273,7 +3273,7 @@ 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. + 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 @@ -3289,7 +3289,7 @@ 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. + 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 @@ -3305,7 +3305,7 @@ quaternary pump system - A pump system that pump and mix up to four different solvents in parallel. + 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 @@ -3320,7 +3320,7 @@ 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. + 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 @@ -3335,7 +3335,7 @@ 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. + 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> @@ -3352,7 +3352,7 @@ 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. + 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 @@ -3368,7 +3368,7 @@ 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. + 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 @@ -3385,7 +3385,7 @@ 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. + 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 @@ -3400,7 +3400,7 @@ 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. + 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 @@ -3422,7 +3422,7 @@ 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. + 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 @@ -3438,7 +3438,7 @@ 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. + 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> @@ -3455,7 +3455,7 @@ 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. + 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 @@ -3471,7 +3471,7 @@ indirect detection probe - An NMR probe designed to allow the indirect detection of acquisition nuclei. + 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 @@ -3487,7 +3487,7 @@ 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. + 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 @@ -3503,7 +3503,7 @@ 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. + 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> @@ -3526,7 +3526,7 @@ 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. + 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 @@ -3546,7 +3546,7 @@ 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. + 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 @@ -3567,7 +3567,7 @@ 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 + 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 @@ -3588,7 +3588,7 @@ 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. + 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 @@ -3611,7 +3611,7 @@ 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 + 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 @@ -3631,7 +3631,7 @@ 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 + 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 @@ -3651,7 +3651,7 @@ HeliScope Single Molecule Sequencer - is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry + 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 @@ -3680,7 +3680,7 @@ anticoagulant-containing test tube - A 'blue top' test tube that contains anticoagulant for storing blood specimens' + 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 @@ -3701,7 +3701,7 @@ 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 + 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 @@ -3724,7 +3724,7 @@ 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. + 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 @@ -3750,7 +3750,7 @@ measurement device A ruler, a microarray scanner, a Geiger counter. - A device in which a measure function inheres. + A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device @@ -3770,7 +3770,7 @@ 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 + 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 @@ -3798,7 +3798,7 @@ 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 + 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 @@ -3819,7 +3819,7 @@ calorimeter - A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. + 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 @@ -3845,7 +3845,7 @@ material separation device flow cytometer - A device with a separation function realized in a planed process + A device with a separation function realized in a planed process material separation device @@ -3863,7 +3863,7 @@ 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. + 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 @@ -3884,7 +3884,7 @@ 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. + 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 @@ -3898,7 +3898,7 @@ optical microscope - A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range + 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 @@ -3917,7 +3917,7 @@ 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. + 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 @@ -3943,7 +3943,7 @@ 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). + 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 @@ -3963,7 +3963,7 @@ 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. + 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 @@ -3994,7 +3994,7 @@ vibrotome - A preparation device that uses a vibrating razor blade to cut through tissue. + A preparation device that uses a vibrating razor blade to cut through tissue. vibrotome @@ -4028,7 +4028,7 @@ container - A device that can be used to restrict the location of material entities over time + 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 @@ -4054,7 +4054,7 @@ 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. + 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 @@ -4081,7 +4081,7 @@ 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. + 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 @@ -4094,7 +4094,7 @@ electron microscope - A microscope that produces an image of an object by targeting it with an electron beam + A microscope that produces an image of an object by targeting it with an electron beam electron microscope @@ -4112,7 +4112,7 @@ Faraday cage - A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. + 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 @@ -4139,7 +4139,7 @@ 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. + A device which has a function to emit light. Person:Helen Parkinson OBI light emission device @@ -4165,7 +4165,7 @@ A homogenizer is a perturbation device. - A perturbation device is a device which is designed to perform a perturb function + A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson @@ -4199,7 +4199,7 @@ 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. + 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 @@ -4237,7 +4237,7 @@ angiograph - A device that records the patterns of pulse waves inside blood vessels. + A device that records the patterns of pulse waves inside blood vessels. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/angiograph angiograph @@ -4257,7 +4257,7 @@ 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. + 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 @@ -4283,7 +4283,7 @@ bioreactor - A device or system that supports a biologically active environment. + A device or system that supports a biologically active environment. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Bioreactor bioreactor @@ -4303,7 +4303,7 @@ pH meter - A device that is used to measure the pH (acidity or alkalinity) of a liquid. + 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 @@ -4323,7 +4323,7 @@ digital camera - An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. + 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 @@ -4343,7 +4343,7 @@ 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. + 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 @@ -4357,7 +4357,7 @@ RNA extraction/purification instrument - A device that is used to isolate and collect RNA for subsequent molecular analysis. + A device that is used to isolate and collect RNA for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell RNA extraction/purification instrument @@ -4371,7 +4371,7 @@ 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. + 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 @@ -4391,7 +4391,7 @@ electrophoresis system - A device that moves charged particles through a medium by using an electric field induced by electrodes. + 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 @@ -4411,7 +4411,7 @@ PET synthesizer - A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. + A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. PERSON: Erik Segerdell PERSON: Erik Segerdell PET synthesizer @@ -4431,7 +4431,7 @@ spinning-disk confocal microscope - A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. + 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 @@ -4445,7 +4445,7 @@ DNA synthesizer - An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. + 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 @@ -4459,7 +4459,7 @@ 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. + 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 @@ -4479,7 +4479,7 @@ microplate reader - A measurement device that detects biological, chemical or physical events of samples in microtiter plates. + 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 @@ -4493,7 +4493,7 @@ ELISA microplate reader - A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). + A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate reader @@ -4513,7 +4513,7 @@ spot cutter - A robotic device that is used to excise spots from gels. + A robotic device that is used to excise spots from gels. PERSON: Erik Segerdell PERSON: Erik Segerdell spot cutter @@ -4539,7 +4539,7 @@ microwave synthesis system - A device that is used to apply microwave irradiation to chemical reactions. + 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 @@ -4559,7 +4559,7 @@ densitometer - A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. + 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 @@ -4585,7 +4585,7 @@ automatic staining machine - A device that is used to automatically stain tissue sections on slides or tissue specimens. + A device that is used to automatically stain tissue sections on slides or tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell automatic staining machine @@ -4611,7 +4611,7 @@ 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. + 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 @@ -4631,7 +4631,7 @@ 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. + 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 @@ -4645,7 +4645,7 @@ 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. + 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 @@ -4665,7 +4665,7 @@ perfusion station - A device or system in which perfusion units are integrated. + A device or system in which perfusion units are integrated. PERSON: Erik Segerdell PERSON: Erik Segerdell perfusion station @@ -4691,7 +4691,7 @@ 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. + 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 @@ -4711,7 +4711,7 @@ scintillation counter - A device that is used to measure ionizing radiation. + A device that is used to measure ionizing radiation. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scintillation_counter scintillation counter @@ -4731,7 +4731,7 @@ programmable array microscope - A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. + 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 @@ -4763,7 +4763,7 @@ 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 + 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 @@ -4783,7 +4783,7 @@ microtome knife maker - A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. + 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 @@ -4803,7 +4803,7 @@ 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. + 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 @@ -4829,7 +4829,7 @@ hybridization oven - A device that creates an appropriate environment for nucleic acid hybridization. + A device that creates an appropriate environment for nucleic acid hybridization. PERSON: Erik Segerdell PERSON: Erik Segerdell hybridization oven @@ -4861,7 +4861,7 @@ incubator shaker - An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). + An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). PERSON: Erik Segerdell PERSON: Erik Segerdell incubator shaker @@ -4887,7 +4887,7 @@ small-animal image acquisition device - A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. + 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 @@ -4913,7 +4913,7 @@ infrared image acquisition device - An image acquisition device that is responsive to an infrared emissive target within a given field of view. + 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 @@ -4933,7 +4933,7 @@ 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. + 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 @@ -4953,7 +4953,7 @@ patch clamp device - A device used in electrophysiology that allows the study of single or multiple ion channels in cells. + 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 @@ -4979,7 +4979,7 @@ gel imaging system - A device that is used to acquire images of laboratory gels. + A device that is used to acquire images of laboratory gels. PERSON: Erik Segerdell PERSON: Erik Segerdell gel imaging system @@ -4999,7 +4999,7 @@ protein separation apparatus - A device that is used for the separation of proteins. + A device that is used for the separation of proteins. PERSON: Erik Segerdell PERSON: Erik Segerdell protein separation apparatus @@ -5013,7 +5013,7 @@ 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. + 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 @@ -5033,7 +5033,7 @@ vitrification apparatus - A device that is used to effect the transition of a substance into a glass. + 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 @@ -5059,7 +5059,7 @@ radiography instrument - An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. + 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 @@ -5085,7 +5085,7 @@ radiation measurement device - A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. + 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 @@ -5111,7 +5111,7 @@ lyophilizer - A device that is used to freeze dry material. + A device that is used to freeze dry material. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Freeze_drying lyophilizer @@ -5125,7 +5125,7 @@ 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. + 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 @@ -5145,7 +5145,7 @@ microhardness tester - A hardness testing device that is used in light-optical microscopes. + A hardness testing device that is used in light-optical microscopes. PERSON: Erik Segerdell United States Patent 4611487 microhardness tester @@ -5159,7 +5159,7 @@ multimode microplate reader - A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. + A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. PERSON: Erik Segerdell PERSON: Erik Segerdell multimode microplate reader @@ -5173,7 +5173,7 @@ mechanical balance - A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). + 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 @@ -5187,7 +5187,7 @@ computer cluster - A group of linked computers, working together closely so that in many respects they form a single computer. + 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 @@ -5207,7 +5207,7 @@ microtome knife sharpener - A device that is used to sharpen knives used in microtomy. + A device that is used to sharpen knives used in microtomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife sharpener @@ -5227,7 +5227,7 @@ plate shaker - A device that provides shaking motion for microplates. + A device that provides shaking motion for microplates. PERSON: Erik Segerdell PERSON: Erik Segerdell plate shaker @@ -5247,7 +5247,7 @@ coagulation analyzer - A device for automatically analyzing blood coagulation in a clinical laboratory. + A device for automatically analyzing blood coagulation in a clinical laboratory. PERSON: Erik Segerdell United States Patent 5439646 coagulation analyzer @@ -5267,7 +5267,7 @@ laser capture microdissection microscope - A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. + 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 @@ -5287,7 +5287,7 @@ liquid extraction robot - A liquid handling device that provides automatic liquid extraction. + A liquid handling device that provides automatic liquid extraction. PERSON: Erik Segerdell PERSON: Erik Segerdell liquid extraction robot @@ -5313,7 +5313,7 @@ ultrasound machine - A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. + 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 @@ -5339,7 +5339,7 @@ immunoblot scanner - A device that is used for the imaging of immunoblots. + A device that is used for the imaging of immunoblots. PERSON: Erik Segerdell PERSON: Erik Segerdell immunoblot scanner @@ -5353,7 +5353,7 @@ 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. + 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 @@ -5367,7 +5367,7 @@ 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. + 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 @@ -5381,7 +5381,7 @@ 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. + 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 @@ -5401,7 +5401,7 @@ rocker - A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). + A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). PERSON: Erik Segerdell PERSON: Erik Segerdell rocker @@ -5415,7 +5415,7 @@ 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. + 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 @@ -5435,7 +5435,7 @@ scanning force microscope - A microscope that forms images of surfaces using a physical probe that scans the specimen. + 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 @@ -5449,7 +5449,7 @@ pulsed-field gel electrophoresis system - A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction. + 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 @@ -5469,7 +5469,7 @@ tissue embedding station - A device that is used to perform paraffin embedding of tissue specimens. + A device that is used to perform paraffin embedding of tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell tissue embedding station @@ -5489,7 +5489,7 @@ nucleic acid sequencer - An device that is used to determine the order of nucleotides in nucleic acid sequences. + An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer @@ -5515,7 +5515,7 @@ bead array reader - A device that is used to acquire and image bead array data. + A device that is used to acquire and image bead array data. PERSON: Erik Segerdell PERSON: Erik Segerdell bead array reader @@ -5529,7 +5529,7 @@ real-time PCR machine - An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. + 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 @@ -5561,7 +5561,7 @@ paraffin oven - A device that is used for the warming of paraffin embedding medium. + A device that is used for the warming of paraffin embedding medium. PERSON: Erik Segerdell PERSON: Erik Segerdell paraffin oven @@ -5593,7 +5593,7 @@ 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. + 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 @@ -5613,7 +5613,7 @@ microplate washer - A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? + 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 @@ -5633,7 +5633,7 @@ nucleic acid extraction/purification instrument - A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. + 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 @@ -5647,7 +5647,7 @@ ELISA microplate washer - A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). + A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate washer @@ -5667,7 +5667,7 @@ 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. + 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 @@ -5681,7 +5681,7 @@ DNA extraction/purification instrument - A device that is used to isolate and collect DNA for subsequent molecular analysis. + 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 @@ -5707,7 +5707,7 @@ multichannel pipette - A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. + 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 @@ -5727,7 +5727,7 @@ cell harvester - A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? + 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 @@ -5741,7 +5741,7 @@ portable fluorometer - A compact fluorometer that can be carried or moved with ease. + A compact fluorometer that can be carried or moved with ease. PERSON: Erik Segerdell PERSON: Erik Segerdell portable fluorometer @@ -5755,7 +5755,7 @@ gel electrophoresis system - An electrophoresis system in which an electric field is applied to a gel matrix + 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 @@ -5775,7 +5775,7 @@ 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. + 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 @@ -5795,7 +5795,7 @@ microdissection instrument - A device that is used for the dissection of tissues under magnification. + A device that is used for the dissection of tissues under magnification. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/microdissection microdissection instrument @@ -5815,7 +5815,7 @@ micropipette puller - A device that is used to fabricate glass micropipettes. + A device that is used to fabricate glass micropipettes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Micropipette micropipette puller @@ -5835,7 +5835,7 @@ 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. + 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 @@ -5855,7 +5855,7 @@ digital microscope - A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. + 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 @@ -5881,7 +5881,7 @@ 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. + 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 @@ -5907,7 +5907,7 @@ micropipette - A microinjection device that is used to measure very small volumes of liquids. + A microinjection device that is used to measure very small volumes of liquids. PERSON: Erik Segerdell http://www.answers.com/topic/micropipette micropipette @@ -5927,7 +5927,7 @@ 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. + 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 @@ -5959,7 +5959,7 @@ vacuum oven - A device that heats materials in a vacuum. + A device that heats materials in a vacuum. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum oven @@ -5979,7 +5979,7 @@ slide warmer - A device that is used to heat microscope slides. + A device that is used to heat microscope slides. PERSON: Erik Segerdell PERSON: Erik Segerdell slide warmer @@ -5993,7 +5993,7 @@ capillary electrophoresis instrument - An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. + 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 @@ -6013,7 +6013,7 @@ 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. + 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 @@ -6027,7 +6027,7 @@ 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. + 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 @@ -6053,7 +6053,7 @@ balance - A measuring instrument that is used to determine the weight or mass of an object. + 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 @@ -6073,7 +6073,7 @@ 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. + 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 @@ -6093,7 +6093,7 @@ protein sequencer - An device that is used to determine the order of amino acids in protein sequences. + An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer @@ -6113,7 +6113,7 @@ X-ray source - A device that is used to generate X-rays. + A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator @@ -6128,7 +6128,7 @@ 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 + 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 @@ -6142,7 +6142,7 @@ SNP microarray - A DNA microarray used to detect polymorphisms in DNA samples + A DNA microarray used to detect polymorphisms in DNA samples Person: Helen Parkinson EFO_0002703 SNP array SNP microarray @@ -6156,7 +6156,7 @@ 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. + 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 @@ -6176,7 +6176,7 @@ - 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. + 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 @@ -6195,7 +6195,7 @@ - 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. + 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 @@ -6248,7 +6248,7 @@ - A BeadChip made for an analyte assay that generates information about DNA methylation. + 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 @@ -6267,7 +6267,7 @@ - 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. + 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 @@ -6280,7 +6280,7 @@ 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. + 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 @@ -6297,7 +6297,7 @@ 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. + 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 @@ -6314,7 +6314,7 @@ 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. + 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 @@ -6331,7 +6331,7 @@ 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. + 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 @@ -6349,7 +6349,7 @@ 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. + 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 @@ -6371,7 +6371,7 @@ 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. + 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 @@ -6392,7 +6392,7 @@ 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. + 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 @@ -6413,7 +6413,7 @@ 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. + 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 @@ -6428,7 +6428,7 @@ 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. + 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 @@ -6443,7 +6443,7 @@ 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. + 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 @@ -6458,7 +6458,7 @@ 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. + 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 @@ -6479,7 +6479,7 @@ 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. + 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 @@ -6500,7 +6500,7 @@ 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. + 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 @@ -6521,7 +6521,7 @@ 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. + 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 @@ -6542,7 +6542,7 @@ 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. + 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 @@ -6563,7 +6563,7 @@ 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. + 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 @@ -6584,7 +6584,7 @@ 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. + 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/ @@ -6605,7 +6605,7 @@ 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. + 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 @@ -6623,7 +6623,7 @@ - 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. + 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 @@ -6642,7 +6642,7 @@ - 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. + 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 @@ -6661,7 +6661,7 @@ - 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. + 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 @@ -6682,7 +6682,7 @@ - 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. + 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 @@ -6702,7 +6702,7 @@ - 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 + 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 @@ -6723,7 +6723,7 @@ - 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. + 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 @@ -6738,7 +6738,7 @@ - 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. + 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 @@ -6767,7 +6767,7 @@ 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 + 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 @@ -6789,7 +6789,7 @@ - A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + 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 @@ -6809,7 +6809,7 @@ - A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + 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 @@ -6841,7 +6841,7 @@ specimen container COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube - A container with the function of containing a specimen. + 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 @@ -6867,7 +6867,7 @@ physical store a freezer. a humidity controlled box. - A container with an environmental control function. + 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 @@ -6887,7 +6887,7 @@ - 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. + 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 @@ -6903,7 +6903,7 @@ 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. + 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 @@ -6918,7 +6918,7 @@ Illumina HiSeq X Ten - A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + 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 @@ -6933,7 +6933,7 @@ 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. + 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 @@ -6947,7 +6947,7 @@ Illumina Infinium MethylationEPIC v1.0 BeadChip - An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. + 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 v1.0 BeadChip @@ -6961,7 +6961,7 @@ 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. + 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 @@ -6976,7 +6976,7 @@ 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. + 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 @@ -6991,7 +6991,7 @@ microtome blade - A device that is the part of a microtome used to slice specimens to a desired thickness. + 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 @@ -7006,7 +7006,7 @@ 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. + 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 @@ -7020,7 +7020,7 @@ microraft - A material separation device also commerically known as Isoraft, that is used to isolate single cells. + 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 @@ -7033,7 +7033,7 @@ 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. + 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 @@ -7053,7 +7053,7 @@ 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. + 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 @@ -7072,7 +7072,7 @@ 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). + 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 @@ -7094,7 +7094,7 @@ 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. + 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 @@ -7109,7 +7109,7 @@ 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 + 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 @@ -7125,7 +7125,7 @@ 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. + 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 @@ -7148,7 +7148,7 @@ 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. + 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 @@ -7169,7 +7169,7 @@ glass bottle - A container with a narrow neck that is made of glass. + A container with a narrow neck that is made of glass. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 @@ -7191,7 +7191,7 @@ glass bottle coated with insecticides - A glass bottle that coated with material designed to control insects. + A glass bottle that coated with material designed to control insects. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 @@ -7214,7 +7214,7 @@ 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. + 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 @@ -7236,7 +7236,7 @@ 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. + 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 @@ -7258,7 +7258,7 @@ 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. + 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 @@ -7275,7 +7275,7 @@ 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. + 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 @@ -7293,7 +7293,7 @@ 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. + 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 @@ -7311,7 +7311,7 @@ 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. + 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 @@ -7328,7 +7328,7 @@ 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. + 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 @@ -7344,7 +7344,7 @@ 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. + 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 @@ -7363,7 +7363,7 @@ 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. + 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 @@ -7380,7 +7380,7 @@ patient gown - A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. + 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 @@ -7397,7 +7397,7 @@ 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. + 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) @@ -7413,7 +7413,7 @@ reusable patient gown - A patient gown intended to be reused after being laundered. + 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 @@ -7428,7 +7428,7 @@ disposable patient gown - A patient gown intended for a single period of continuous use and then disposed of. + 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 @@ -7443,7 +7443,7 @@ 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. + 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 @@ -7459,7 +7459,7 @@ apron - A garment which is worn over other clothing and covers mainly the front of the body. + 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 @@ -7474,7 +7474,7 @@ 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. + 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 @@ -7489,7 +7489,7 @@ personal protective glove - A personal protective device which is a 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 @@ -7504,7 +7504,7 @@ 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. + 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 @@ -7519,7 +7519,7 @@ laboratory coat - A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. + 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 @@ -7535,7 +7535,7 @@ 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. + 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 @@ -7550,7 +7550,7 @@ nitrile glove - A personal protective glove which is made out of nitrile rubber. + 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 @@ -7565,7 +7565,7 @@ 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. + 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 @@ -7581,7 +7581,7 @@ 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. + 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 @@ -7598,7 +7598,7 @@ disposable footwear cover - A footwear cover which is designed for a single period of continuous use and then disposed of. + 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 @@ -7613,7 +7613,7 @@ reusable footwear cover - A footwear cover which is designed for repeated use. + 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 @@ -7628,7 +7628,7 @@ surgical N95 respirator - A N95 respirator which has been approved by the FDA as a surgical mask. + 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 @@ -7647,7 +7647,7 @@ 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. + 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 @@ -7663,7 +7663,7 @@ 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. + 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 @@ -7678,7 +7678,7 @@ protective apron - A personal protective clothing item which is an 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 @@ -7693,7 +7693,7 @@ medical cap - A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. + 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 @@ -7713,7 +7713,7 @@ specimen collection device - A device used to collect a specimen. + A device used to collect a specimen. https://orcid.org/0000-0002-8844-9165 specimen collection device @@ -7726,7 +7726,7 @@ chromatography vial - A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography. + 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 @@ -7742,7 +7742,7 @@ 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. + 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 @@ -7764,7 +7764,7 @@ 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. + 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 @@ -7782,7 +7782,7 @@ cotton swab - A device which is a cotton pad mounted on one or both ends of a stick. + 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 @@ -7804,7 +7804,7 @@ 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 + 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 @@ -7818,7 +7818,7 @@ pre-moistened swab stick - A specimen collection swab stick that is pre-moistened with liquid prior to sampling. + 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 @@ -7832,7 +7832,7 @@ 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. + 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 @@ -7847,7 +7847,7 @@ catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. - A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. + A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. https://orcid.org/0000-0002-8844-9165 http://purl.bioontology.org/ontology/MESH/D057785 catheter @@ -7861,7 +7861,7 @@ ultraviolet light source - A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. + 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 @@ -7878,7 +7878,7 @@ visible light source - A light source that provides visible light for use in a distant area using a delivery system. + 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 @@ -7894,7 +7894,7 @@ solar light source - A light source that light is produced from solar energy. + A light source that light is produced from solar energy. Person: Chris Stoeckert Person: Jie Zheng Person: Chris Stoeckert @@ -7916,7 +7916,7 @@ - A device designed to catch arthropods. + A device designed to catch arthropods. John Judkins MIRO:30000011 https://github.com/obi-ontology/obi/issues/1217 @@ -7929,7 +7929,7 @@ - An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. + 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 @@ -7942,7 +7942,7 @@ - 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. + 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 @@ -7954,7 +7954,7 @@ - An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. + 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 @@ -7973,7 +7973,7 @@ - A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. + 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 @@ -7992,7 +7992,7 @@ - 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. + 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 @@ -8006,7 +8006,7 @@ - A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery. + A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. John Judkins CDC light trap @@ -8021,7 +8021,7 @@ - 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. + 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 @@ -8035,7 +8035,7 @@ - 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. + 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 @@ -8050,7 +8050,7 @@ - An arthropod trap that is designed to collect gravid female arthropods or their eggs. + 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 @@ -8063,7 +8063,7 @@ - An arthropod trap that uses light as an attractant. + An arthropod trap that uses light as an attractant. John Judkins MIRO:30000065 https://github.com/obi-ontology/obi/issues/1217 @@ -8076,7 +8076,7 @@ - A light trap designed to be placed inside a building. + A light trap designed to be placed inside a building. John Judkins indoor light trap MIRO:30000009 @@ -8090,7 +8090,7 @@ - A light trap designed to be placed outside a building. + A light trap designed to be placed outside a building. John Judkins outdoor light trap MIRO:30000010 @@ -8104,7 +8104,7 @@ - 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. + 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 @@ -8117,7 +8117,7 @@ - A gravid trap consisting of an arthropod attractant and adhesive surface. + A gravid trap consisting of an arthropod attractant and adhesive surface. John Judkins IRO:0000140 https://github.com/obi-ontology/obi/issues/1217 @@ -8130,7 +8130,7 @@ - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. + 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 @@ -8144,7 +8144,7 @@ - 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. + 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 @@ -8159,7 +8159,7 @@ - An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. + 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 @@ -8173,7 +8173,7 @@ - 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. + 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 @@ -8188,7 +8188,7 @@ - An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. + 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 @@ -8200,7 +8200,7 @@ - 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. + 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 @@ -8214,7 +8214,7 @@ - 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). + 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 @@ -8228,7 +8228,7 @@ - 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. + 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 @@ -8242,7 +8242,7 @@ - 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. + 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 @@ -8256,7 +8256,7 @@ - An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. + 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 @@ -8270,7 +8270,7 @@ - A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. + A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. John Judkins VSMO:0001355 https://github.com/obi-ontology/obi/issues/1302 @@ -8284,7 +8284,7 @@ - A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. + A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB @@ -8297,7 +8297,7 @@ - An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller. + An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller. John Judkins trap containing small non-human animal bait VSMO:0001595 @@ -8312,7 +8312,7 @@ - An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. + An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. John Judkins American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389 VSMO:0001352 @@ -8328,7 +8328,7 @@ 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. + 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 @@ -8346,7 +8346,7 @@ - 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. + 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 @@ -8359,7 +8359,7 @@ - A device that consists of a network of mesh and is designed to capture adult arthropods. + A device that consists of a network of mesh and is designed to capture adult arthropods. VEuPathDB VSMO:0001522 hand-held sweep net @@ -8372,7 +8372,7 @@ 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. + 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 @@ -8393,7 +8393,7 @@ 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. + 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 @@ -8406,7 +8406,7 @@ - A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. + 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 https://github.com/obi-ontology/obi/issues/1439 @@ -8421,7 +8421,7 @@ assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf - A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. + A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. John Judkins OBI, VEuPathDB https://github.com/obi-ontology/obi/issues/1456 @@ -8442,7 +8442,7 @@ Illumina HiSeq 1500 - A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8466,7 +8466,7 @@ NextSeq 550 - A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. + A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8489,7 +8489,7 @@ Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 - A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays. + A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8512,7 +8512,7 @@ Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray - A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays. + A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8535,7 +8535,7 @@ Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray - A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays. + A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8558,7 +8558,7 @@ Affymetrix Mouse Genome 430 2.0 Array - A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database. + A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8582,7 +8582,7 @@ Affymetrix Mouse Genome 430A 2.0 Array - A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database. + A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8606,7 +8606,7 @@ Affymetrix Mouse Gene 1.0 ST Array - A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. + A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8630,7 +8630,7 @@ Affymetrix Mouse Gene 2.1 ST Array - A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db. + A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8654,7 +8654,7 @@ Affymetrix Rhesus Macaque Genome Array - A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response. + A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8678,7 +8678,7 @@ Affymetrix Human Transcriptome Array 2.0 - A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome. + A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8702,7 +8702,7 @@ Affymetrix Human Genome U219 Array - A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™. + A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8726,7 +8726,7 @@ Affymetrix Human Gene 2.0 ST Array - A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events. + A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8750,7 +8750,7 @@ Affymetrix Clariom S Assay, Human - A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways. + A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8773,7 +8773,7 @@ Affymetrix Clariom S Assay, Mouse - A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways. + A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8796,7 +8796,7 @@ Illumina HumanHT-12 V4.0 expression beadchip - An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants. + An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8819,7 +8819,7 @@ Illumina MouseRef-8 v2.0 beadchip - An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content. + An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8842,7 +8842,7 @@ Affymetrix Mouse Exon Junction Array - A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome. + A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8865,7 +8865,7 @@ Affymetrix Human Exon Junction Array - A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome. + A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome. Jain Aluvathingal Michelle Giglio Suvarna Nadendla @@ -8881,7 +8881,7 @@ - An arthropod trap that 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. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor. + An arthropod trap that 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. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor. VEuPathDB https://github.com/obi-ontology/obi/issues/1523 Mosquito Magnet Liberty Plus trap @@ -8899,7 +8899,7 @@ - A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent. + A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent. John Judkins ORCID:0000-0001-6595-0902 Sarah Kelly https://github.com/obi-ontology/obi/issues/1602 @@ -8924,7 +8924,7 @@ - An assay kit that is manufactured by InBios International to use ELISA to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716, with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen. + An assay kit that is manufactured by InBios International to use ELISA to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716, with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen. John Judkins ORCID:0000-0001-6595-0902 https://inbios.com/scrub-typhus-detecttm-igm-elisa-kit-intl/ Scrub Typhus Detect IgM ELISA kit @@ -8948,7 +8948,7 @@ - An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody. + An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody. John Judkins ORCID:0000-0001-6595-0902 Panbio Dengue IgM capture ELISA kit @@ -8971,7 +8971,7 @@ - An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody. + An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody. John Judkins ORCID:0000-0001-6595-0902 Panbio Dengue Early ELISA kit @@ -8994,7 +8994,7 @@ - A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography. + A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography. John Judkins ORCID:0000-0001-6595-0902 https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html SD Bioline Chikungunya IgM RDT kit @@ -9018,7 +9018,7 @@ - An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA. + An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA. John Judkins ORCID:0000-0001-6595-0902 SD Bioline Chikungunya IgM capture ELISA kit @@ -9041,7 +9041,7 @@ - An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA. + An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA. John Judkins ORCID:0000-0001-6595-0902 Advantage Chikungunya IgM Card kit @@ -9088,7 +9088,7 @@ - A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap. + A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap. John Judkins ORCID:0000-0001-6595-0902 human odour baited light trap VEuPathDB @@ -9102,7 +9102,7 @@ - A resting arthropod trap that consists of a container composed primarily of clay. + A resting arthropod trap that consists of a container composed primarily of clay. John Judkins ORCID:0000-0001-6595-0902 resting clay pot catch https://github.com/obi-ontology/obi/issues/1651 @@ -9121,7 +9121,7 @@ - A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. Sebastian Duesing NextSeq 1000 https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html @@ -9137,7 +9137,7 @@ Illumina Infinium MethylationEPIC v2.0 BeadChip - An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. + An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. Sebastian Duesing https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html https://github.com/obi-ontology/obi/issues/1665 @@ -9158,7 +9158,7 @@ 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. + 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 @@ -9172,7 +9172,7 @@ 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. + 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 @@ -9193,7 +9193,7 @@ 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. + 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 @@ -9241,7 +9241,7 @@ 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. + 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 @@ -9256,7 +9256,7 @@ 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. + 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 @@ -9271,7 +9271,7 @@ 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. + 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 @@ -9287,7 +9287,7 @@ 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. + 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 @@ -9301,7 +9301,7 @@ 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. + 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 @@ -9316,7 +9316,7 @@ 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. + 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 @@ -9331,7 +9331,7 @@ 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. + 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 @@ -9346,7 +9346,7 @@ 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. + 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 @@ -9361,7 +9361,7 @@ 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. + 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 @@ -9376,7 +9376,7 @@ 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. + 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 @@ -9390,7 +9390,7 @@ 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. + 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 @@ -9417,7 +9417,7 @@ 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. + 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 @@ -9432,7 +9432,7 @@ 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. + 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 @@ -9446,7 +9446,7 @@ 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. + 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 @@ -9460,7 +9460,7 @@ 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. + 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 @@ -9474,7 +9474,7 @@ 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. + 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 @@ -9488,7 +9488,7 @@ 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. + 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 @@ -9503,7 +9503,7 @@ 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. + 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 @@ -9524,7 +9524,7 @@ 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. + 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 @@ -9538,7 +9538,7 @@ 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. + 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 @@ -9552,7 +9552,7 @@ 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. + 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 @@ -9567,7 +9567,7 @@ 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. + 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 @@ -9582,7 +9582,7 @@ 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. + 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 @@ -9603,7 +9603,7 @@ 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. + 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 @@ -9618,7 +9618,7 @@ 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. + 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 @@ -9633,7 +9633,7 @@ 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. + 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 @@ -9649,7 +9649,7 @@ FACS Calibur FACS Calibur at TFL, BCCRC, Vancouver - The FACS Calibur is one of the most popular cytometers in use for research. + 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 @@ -9663,7 +9663,7 @@ 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. + 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 @@ -9677,7 +9677,7 @@ 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. + 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 @@ -9691,7 +9691,7 @@ 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. + 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 @@ -9706,7 +9706,7 @@ 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. + 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 @@ -9721,7 +9721,7 @@ 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. + 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 @@ -9735,7 +9735,7 @@ 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. + 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 @@ -9756,7 +9756,7 @@ 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. + 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 @@ -9808,7 +9808,7 @@ 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. + 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 @@ -9835,7 +9835,7 @@ 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. + 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 @@ -9850,7 +9850,7 @@ 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. + 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 @@ -9865,7 +9865,7 @@ 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. + 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 @@ -9879,7 +9879,7 @@ 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. + 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 @@ -9893,7 +9893,7 @@ 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. + 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 @@ -9908,7 +9908,7 @@ 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. + 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 @@ -9924,7 +9924,7 @@ 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. + 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 @@ -9939,7 +9939,7 @@ 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. + 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 @@ -9966,7 +9966,7 @@ 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. + 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 @@ -9982,7 +9982,7 @@ 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. + 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 @@ -9997,7 +9997,7 @@ 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. + 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 @@ -10012,7 +10012,7 @@ 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. + 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 @@ -10028,7 +10028,7 @@ 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. + 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 @@ -10043,7 +10043,7 @@ 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. + 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 @@ -10059,7 +10059,7 @@ 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. + 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 @@ -10081,7 +10081,7 @@ 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. + 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 @@ -10098,7 +10098,7 @@ 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. + 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 @@ -10113,7 +10113,7 @@ 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. + 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 @@ -10128,7 +10128,7 @@ 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. + 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 @@ -10142,7 +10142,7 @@ 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. + 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 @@ -10156,7 +10156,7 @@ 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 + 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 @@ -10170,7 +10170,7 @@ 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. + 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 @@ -10185,7 +10185,7 @@ 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. + 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 @@ -10200,7 +10200,7 @@ 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. + 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 @@ -10215,7 +10215,7 @@ 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. + 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 @@ -10230,7 +10230,7 @@ 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. + 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 @@ -10251,7 +10251,7 @@ 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. + 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 @@ -10273,7 +10273,7 @@ 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. + 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 @@ -10306,7 +10306,7 @@ 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. + 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 @@ -10328,7 +10328,7 @@ 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. + 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 @@ -10343,7 +10343,7 @@ 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. + 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 @@ -10376,7 +10376,7 @@ 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. + 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 @@ -10397,7 +10397,7 @@ 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. + 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 @@ -10413,7 +10413,7 @@ 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. + 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 @@ -10428,7 +10428,7 @@ 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. + 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 @@ -10443,7 +10443,7 @@ 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. + 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 @@ -10458,7 +10458,7 @@ 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. + 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 @@ -10485,7 +10485,7 @@ 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. + 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 @@ -10500,7 +10500,7 @@ 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. + 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 @@ -10515,7 +10515,7 @@ 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. + 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 @@ -10529,7 +10529,7 @@ 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. + 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 @@ -10544,7 +10544,7 @@ SomaScope SomaScope Mark II Automatic Economical - The SomaScope is an instrument to quantify somatic cells in milk. + 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 @@ -10589,7 +10589,7 @@ 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. + 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 @@ -10617,7 +10617,7 @@ 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. + 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 @@ -10638,7 +10638,7 @@ voltage amplifier Linear amplifier, log amplifier, microwave amplifier - A voltage amplifier is a device that amplifies the voltage signal. + A voltage amplifier is a device that amplifies the voltage signal. Frank Gibson John Quinn http://en.wiktionary.org/wiki/amplifier @@ -10660,7 +10660,7 @@ 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. + 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 @@ -10681,7 +10681,7 @@ 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. + A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer @@ -10708,7 +10708,7 @@ 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 + 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 @@ -10729,7 +10729,7 @@ arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 - A device which deposits biological material onto a substrate in a defined pattern. + A device which deposits biological material onto a substrate in a defined pattern. Trish Whetzel MO_697 arrayer arrayer @@ -10776,7 +10776,7 @@ centrifuge - A device with a rapidly rotating container that applies centrifugal force to its contents + A device with a rapidly rotating container that applies centrifugal force to its contents Melanie Courtot Person: Jennifer Fostel Trish Whetzel @@ -10799,7 +10799,7 @@ computer Apple PowerBook, Dell OptiPlex - A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. + 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 @@ -10821,7 +10821,7 @@ 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 + 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 @@ -10842,7 +10842,7 @@ 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. + 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 @@ -10870,7 +10870,7 @@ 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. + 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 @@ -10897,7 +10897,7 @@ 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. + 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 @@ -10918,7 +10918,7 @@ liquid handler Beckman BioMek 2000 - A device that is used for automated liquid transfer and handling. + 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. @@ -10947,7 +10947,7 @@ oligonucleotide synthesizer Automated Multiplex Oligonucleotide Synthesizer - An instrument used to chemically synthesize oligonucleotides. + An instrument used to chemically synthesize oligonucleotides. Trish Whetzel MO oligonucleotide synthesizer @@ -10968,7 +10968,7 @@ 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. + 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 @@ -10989,7 +10989,7 @@ 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. + 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 @@ -11017,7 +11017,7 @@ 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. + An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. Melanie Courtot Trish Whetzel DNA_amplifier @@ -11055,7 +11055,7 @@ vacuum dryer Model 777 Microarray Oven - An instrument which removes liquid by the application of negative pressure, i.e. vacuum. + An instrument which removes liquid by the application of negative pressure, i.e. vacuum. Trish Whetzel MO vacuum dryer @@ -11076,7 +11076,7 @@ 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. + 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 @@ -11099,7 +11099,7 @@ microarray wash station ArrayIt(r) Microarray Wash Station - A device that is used to wash Affymetrix-type arrays. + A device that is used to wash Affymetrix-type arrays. Trish Whetzel MO_626 wash_station microarray wash station @@ -11126,7 +11126,7 @@ 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. + 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 @@ -11156,7 +11156,7 @@ molecular crosslinker Stratalinker - A device that is able to chemically join two or more molecules. + 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 @@ -11197,7 +11197,7 @@ 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. + 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 @@ -11235,7 +11235,7 @@ cytometer - A cytometer is an instrument for counting and/or measuring characteristics of cells. + A cytometer is an instrument for counting and/or measuring characteristics of cells. Melanie Courtot http://medical.merriam-webster.com/medical/cytometer cytometer @@ -11262,7 +11262,7 @@ 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. + 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 @@ -11286,7 +11286,7 @@ 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. + 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 @@ -11308,7 +11308,7 @@ 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. + 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 @@ -11341,7 +11341,7 @@ 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. + 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/ @@ -11357,7 +11357,7 @@ 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. + 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 @@ -11372,7 +11372,7 @@ 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. + 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 @@ -11390,7 +11390,7 @@ 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. + 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 @@ -11410,7 +11410,7 @@ 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. + 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 @@ -11425,7 +11425,7 @@ 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). + 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 @@ -11440,7 +11440,7 @@ 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). + 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 @@ -11461,7 +11461,7 @@ 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. + 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 @@ -11488,7 +11488,7 @@ 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. + 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 @@ -11515,7 +11515,7 @@ 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) + 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 @@ -11536,7 +11536,7 @@ 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 + 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 @@ -11557,7 +11557,7 @@ 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. + 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 diff --git a/src/ontology/modules/epitope-assays.owl b/src/ontology/modules/epitope-assays.owl index 15c3a55c..04366946 100644 --- a/src/ontology/modules/epitope-assays.owl +++ b/src/ontology/modules/epitope-assays.owl @@ -865,7 +865,7 @@ - An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. + 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 @@ -903,7 +903,7 @@ - A cytometric bead array assay that detects IP-10 production by T cells. + 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 @@ -941,7 +941,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -979,7 +979,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells. + 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 @@ -1017,7 +1017,7 @@ - An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells. + 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 @@ -1055,7 +1055,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1093,7 +1093,7 @@ - A cytometric bead array assay that detects transforming growth factor-beta production by T cells + 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 @@ -1131,7 +1131,7 @@ - A flow cytometry assay that detects epitope specific perforin release by T cells. + A flow cytometry assay that detects epitope specific perforin release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|intracellular staining @@ -1169,7 +1169,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells. + 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 @@ -1207,7 +1207,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1245,7 +1245,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1283,7 +1283,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells. + 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 @@ -1321,7 +1321,7 @@ - An enzyme-linked immunosorbent assay that detects RANTES production by T cells. + An enzyme-linked immunosorbent assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ELISA @@ -1359,7 +1359,7 @@ - A cytometric bead array assay that detects interleukin-1 beta production by T cells. + 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 @@ -1397,7 +1397,7 @@ - An enzyme-linked immunospot assay that detects interleukin-6 production by T cells + 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 @@ -1459,7 +1459,7 @@ - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody 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|in vivo assay @@ -1500,7 +1500,7 @@ - A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor. + 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 @@ -1538,7 +1538,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1576,7 +1576,7 @@ - An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells. + 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 @@ -1614,7 +1614,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1652,7 +1652,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1690,7 +1690,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells. + 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 @@ -1728,7 +1728,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -1766,7 +1766,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells. + 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 @@ -1804,7 +1804,7 @@ - A flow cytometry assay that detects interleukin-6 production by T cells. + A flow cytometry assay that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|ICS @@ -1842,7 +1842,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells. + 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 @@ -1880,7 +1880,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells. + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|RNA/DNA detection @@ -1918,7 +1918,7 @@ - A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells. + 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 @@ -1956,7 +1956,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells. + 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 @@ -1994,7 +1994,7 @@ - A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. + A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|RNA/DNA detection @@ -2032,7 +2032,7 @@ - An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells. + 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 @@ -2070,7 +2070,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -2108,7 +2108,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -2146,7 +2146,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells. + 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 @@ -2184,7 +2184,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells. + 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 @@ -2222,7 +2222,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells. + 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 @@ -2284,7 +2284,7 @@ - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell 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|in vivo assay @@ -2322,7 +2322,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -2360,7 +2360,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells. + 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 @@ -2401,7 +2401,7 @@ - A T cell epitope dependent biological activity assay that detects 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 @@ -2439,7 +2439,7 @@ - A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells. + 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 @@ -2477,7 +2477,7 @@ - An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells. + 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 @@ -2515,7 +2515,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells. + 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 @@ -2553,7 +2553,7 @@ - A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 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 @@ -2591,7 +2591,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells. + 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 @@ -2629,7 +2629,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells. + 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 @@ -2667,7 +2667,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -2705,7 +2705,7 @@ - An enzyme-linked immunosorbent assay that detects IP-10 production by T cells. + 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 @@ -2743,7 +2743,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells. + 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 @@ -2781,7 +2781,7 @@ - A cytometric bead array assay that detects interleukin-12 production by T cells. + 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 @@ -2819,7 +2819,7 @@ - An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells. + 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 @@ -2857,7 +2857,7 @@ - A cytometric bead array assay that detects interleukin-5 production by T cells. + 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 @@ -2895,7 +2895,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells. + 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 @@ -2933,7 +2933,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -2971,7 +2971,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -3009,7 +3009,7 @@ - A cytometric bead array assay that detects interleukin-17 production by T cells. + 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 @@ -3047,7 +3047,7 @@ - A cytometric bead array assay that detects interleukin-10 production by T cells. + A cytometric bead array assay that detects interleukin-10 production by T cells. IEDB IEDB IL-10 release|cytometric bead array @@ -3085,7 +3085,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells. + 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 @@ -3123,7 +3123,7 @@ - A flow cytometry assay that detects interleukin-5 production by T cells. + A flow cytometry assay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|ICS @@ -3161,7 +3161,7 @@ - A cytometric bead array assay that detects interleukin-2 production by T cells. + 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 @@ -3199,7 +3199,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells. + 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 @@ -3237,7 +3237,7 @@ - An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells. + 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 @@ -3275,7 +3275,7 @@ - A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells. + 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 @@ -3313,7 +3313,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -3351,7 +3351,7 @@ - A flow cytometry assay that detects interleukin-13 production by T cells. + A flow cytometry assay that detects interleukin-13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|ICS @@ -3392,7 +3392,7 @@ - A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. + 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 @@ -3430,7 +3430,7 @@ - An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. + 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 @@ -3460,7 +3460,7 @@ - A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. + 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 @@ -3498,7 +3498,7 @@ - A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. + 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 @@ -3536,7 +3536,7 @@ - An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. + An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISPOT @@ -3598,7 +3598,7 @@ - An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. + 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 @@ -3636,7 +3636,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. + 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 @@ -3674,7 +3674,7 @@ - A cytometric bead array assay that detects interleukin-4 production by T cells + 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 @@ -3712,7 +3712,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -3750,7 +3750,7 @@ - An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. IEDB IEDB CXCL9/MIG release|ELISA @@ -3788,7 +3788,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -3826,7 +3826,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells. + 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 @@ -3864,7 +3864,7 @@ - A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells. + 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 @@ -3902,7 +3902,7 @@ - A flow cytometry assay that detects interleukin-21 production by T cells. + A flow cytometry assay that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ICS @@ -3940,7 +3940,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells. + 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 @@ -3978,7 +3978,7 @@ - An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells. + 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 @@ -4016,7 +4016,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -4054,7 +4054,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. + 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 @@ -4116,7 +4116,7 @@ - An efficacy of T cell epitope intervention experiment that detects 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 @@ -4154,7 +4154,7 @@ - A cytometric bead array assay that detects interleukin-13 production by T cells. + 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 @@ -4192,7 +4192,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. + 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 @@ -4230,7 +4230,7 @@ - A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. + A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|cytometric bead array @@ -4268,7 +4268,7 @@ - An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. + 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 @@ -4306,7 +4306,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. + 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 @@ -4344,7 +4344,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells. + 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 @@ -4382,7 +4382,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells. + 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 @@ -4420,7 +4420,7 @@ - A cytometric bead array assay that detects interleukin-6 production by T cells. + 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 @@ -4458,7 +4458,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -4496,7 +4496,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells. + 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 @@ -4534,7 +4534,7 @@ - A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells. + 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 @@ -4572,7 +4572,7 @@ - A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. + 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 @@ -4610,7 +4610,7 @@ - A flow cytometry assay that detects interleukin-3 production by T cells. + A flow cytometry assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ICS @@ -4648,7 +4648,7 @@ - An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. + 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 @@ -4686,7 +4686,7 @@ - A cytometric bead array assay that detects interferon-gamma production by T cells. + 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 @@ -4724,7 +4724,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -4762,7 +4762,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. + 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 @@ -4800,7 +4800,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. + 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 @@ -4838,7 +4838,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells. + 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 @@ -4876,7 +4876,7 @@ - A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells. + 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 @@ -4914,7 +4914,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -4952,7 +4952,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells. + 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 @@ -4990,7 +4990,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5028,7 +5028,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5090,7 +5090,7 @@ - An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. + An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB cytotoxicity|in vivo assay @@ -5128,7 +5128,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells. + 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 @@ -5166,7 +5166,7 @@ - A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells. + 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 @@ -5204,7 +5204,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5242,7 +5242,7 @@ - A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. + A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. IEDB IEDB IL-2 release|reporter gene assay @@ -5280,7 +5280,7 @@ - A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells. + 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 @@ -5318,7 +5318,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5356,7 +5356,7 @@ - A T cell epitope dependent biological activity assay that detects T cell activation. + A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB activation|biological activity @@ -5394,7 +5394,7 @@ - A cytometric bead array assay that detects RANTES production by T cells. + 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 @@ -5432,7 +5432,7 @@ - A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. + 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 @@ -5470,7 +5470,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5508,7 +5508,7 @@ - An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. + An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|biological activity @@ -5546,7 +5546,7 @@ - A flow cytometry assay that detects epitope specific granzyme B release by T cells + A flow cytometry assay that detects epitope specific granzyme B release by T cells PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|intracellular staining @@ -5584,7 +5584,7 @@ - A radio immuno assay that detects interferon-gamma production by T cells. + 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) @@ -5622,7 +5622,7 @@ - A T cell epitope specific cytotoxic T cell degranulation assay that detects 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 @@ -5660,7 +5660,7 @@ - A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + 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 @@ -5698,7 +5698,7 @@ - An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. + 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 @@ -5736,7 +5736,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5774,7 +5774,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5812,7 +5812,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5850,7 +5850,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -5888,7 +5888,7 @@ - A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells. + A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|bioassay @@ -5926,7 +5926,7 @@ - A flow cytometry assay that detects lymphotoxin A production by T cells. + 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 @@ -5964,7 +5964,7 @@ - An enzyme-linked immunospot assay that detects interleukin-5 production by T cells. + 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 @@ -6002,7 +6002,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -6040,7 +6040,7 @@ - A cytometric bead array assay that detects interleukin-8 production by T cells. + 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 @@ -6078,7 +6078,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -6116,7 +6116,7 @@ - An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. + An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISA @@ -6154,7 +6154,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -6192,7 +6192,7 @@ - A flow cytometry assay that detects interleukin-12 production by T cells. + A flow cytometry assay that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|ICS @@ -6249,7 +6249,7 @@ - An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. IEDB IEDB disease exacerbation|in vivo assay @@ -6275,7 +6275,7 @@ - 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. + 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 @@ -6340,7 +6340,7 @@ - An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden. + An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay @@ -6405,7 +6405,7 @@ - An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay @@ -6441,7 +6441,7 @@ - A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands + A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands IEDB IEDB ligand presentation|mass spectrometry @@ -6479,7 +6479,7 @@ - A flow cytometry assay that detects transforming growth factor-beta production by T cells. + A flow cytometry assay that detects transforming growth factor-beta production by T cells. IEDB IEDB TGFb release|ICS @@ -6536,7 +6536,7 @@ - A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. + A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. IEDB IEDB in vivo activity|biological activity @@ -6574,7 +6574,7 @@ - A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. + A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. IEDB IEDB ligand presentation|cellular MHC/mass spectrometry @@ -6612,7 +6612,7 @@ - A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells. + 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 @@ -6694,7 +6694,7 @@ - An in vivo assay measuring T cell epitope specific protection from other challenge using survival. + An in vivo assay measuring T cell epitope specific protection from other challenge using survival. IEDB IEDB survival from challenge|in vivo assay @@ -6769,7 +6769,7 @@ - A cell bound MHC binding assay that uses a T cell epitope recognition assay. + A cell bound MHC binding assay that uses a T cell epitope recognition assay. IEDB IEDB qualitative binding|cellular MHC/T cell inhibition @@ -6831,7 +6831,7 @@ - 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. + 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|in vivo assay @@ -6869,7 +6869,7 @@ - A flow cytometry assay that detects interleukin-22 production by T cells. + A flow cytometry assay that detects interleukin-22 production by T cells. IEDB IEDB IL-22 release|ICS @@ -6907,7 +6907,7 @@ - A T cell epitope specific cytotoxic T cell degranulation assay that detects 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 @@ -6955,7 +6955,7 @@ - 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. + 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 @@ -7022,7 +7022,7 @@ - An efficacy of T cell epitope intervention experiment that detects a decrease in disease. + An efficacy of T cell epitope intervention experiment that detects a decrease in disease. IEDB IEDB decreased disease|in vivo assay @@ -7052,7 +7052,7 @@ - A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands + 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 @@ -7078,7 +7078,7 @@ - A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. + A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. IEDB IEDB ligand presentation|secreted MHC/mass spectrometry @@ -7116,7 +7116,7 @@ - A cytometric bead array assay that detects interleukin-17A production by T cells. + A cytometric bead array assay that detects interleukin-17A production by T cells. IEDB IEDB IL-17A release|cytometric bead array @@ -7178,7 +7178,7 @@ - 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. + 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 @@ -7233,7 +7233,7 @@ - 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. + 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 @@ -7302,7 +7302,7 @@ - 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. + 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 @@ -7348,7 +7348,7 @@ - A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. + 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 @@ -7417,7 +7417,7 @@ - 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. + 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 @@ -7455,7 +7455,7 @@ - An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. + An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. IEDB IEDB G-CSF release|ELISA @@ -7493,7 +7493,7 @@ - A cytometric bead array assay that detects interleukin-17F production by T cells. + A cytometric bead array assay that detects interleukin-17F production by T cells. IEDB IEDB IL-17F release|cytometric bead array @@ -7548,7 +7548,7 @@ - A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -7603,7 +7603,7 @@ - A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. + 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 @@ -7641,7 +7641,7 @@ - A cytometric bead array assay that detects interleukin-9 production by T cells. + A cytometric bead array assay that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|cytometric bead array @@ -7703,7 +7703,7 @@ - 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. + 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 @@ -7778,7 +7778,7 @@ - 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. + 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 @@ -7847,7 +7847,7 @@ - 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. + 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 @@ -7902,7 +7902,7 @@ - A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex. + 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 @@ -7940,7 +7940,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells. + 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 @@ -7995,7 +7995,7 @@ - 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. + 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 @@ -8064,7 +8064,7 @@ - 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. + 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 @@ -8102,7 +8102,7 @@ - A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. + A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. IEDB IEDB CCL3/MIP-1a release|ICS @@ -8177,7 +8177,7 @@ - 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. + 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 @@ -8223,7 +8223,7 @@ - A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -8261,7 +8261,7 @@ - A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells. + 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 @@ -8293,7 +8293,7 @@ - A MHC:ligand binding assay that measures a binding constant. + A MHC:ligand binding assay that measures a binding constant. IEDB IEDB binding constant|binding assay @@ -8339,7 +8339,7 @@ - A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand. + 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 @@ -8385,7 +8385,7 @@ - A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. + 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 @@ -8440,7 +8440,7 @@ - A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -8495,7 +8495,7 @@ - A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -8550,7 +8550,7 @@ - A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -8588,7 +8588,7 @@ - A flow cytometry assay that detects interleukin-17F production by T cells. + A flow cytometry assay that detects interleukin-17F production by T cells. IEDB IEDB IL-17F release|ICS @@ -8657,7 +8657,7 @@ - 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. + 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 @@ -8712,7 +8712,7 @@ - A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand. + 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 @@ -8773,7 +8773,7 @@ - A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand. + 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 @@ -8842,7 +8842,7 @@ - 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. + 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 @@ -8897,7 +8897,7 @@ - A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand. + 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 @@ -8935,7 +8935,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -8979,7 +8979,7 @@ - A cytometric bead array assay that detects interleukin-22 production by T cells. + A cytometric bead array assay that detects interleukin-22 production by T cells. IEDB IEDB IL-22 release|cytometric bead array @@ -9017,7 +9017,7 @@ - An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. + An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|ELISA @@ -9063,7 +9063,7 @@ - A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand. + 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 @@ -9121,7 +9121,7 @@ - A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand. + 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 @@ -9159,7 +9159,7 @@ - A cytometric bead array assay that detects interleukin-7 production by T cells. + A cytometric bead array assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|cytometric bead array @@ -9214,7 +9214,7 @@ - A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. + 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 @@ -9252,7 +9252,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -9290,7 +9290,7 @@ - A flow cytometry assay that detects interleukin-17A production by T cells. + A flow cytometry assay that detects interleukin-17A production by T cells. IEDB IEDB IL-17A release|ICS @@ -9336,7 +9336,7 @@ - A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand. + 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 @@ -9391,7 +9391,7 @@ - A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand. + 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 @@ -9453,7 +9453,7 @@ - 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. + 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 @@ -9508,7 +9508,7 @@ - A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. + 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 @@ -9588,7 +9588,7 @@ - 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. + 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 @@ -9650,7 +9650,7 @@ - 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. + 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 @@ -9688,7 +9688,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -9726,7 +9726,7 @@ - A cytometric bead array assay that detects interleukin-21 production by T cells. + A cytometric bead array assay that detects interleukin-21 production by T cells. IEDB IEDB IL-21 release|cytometric bead array @@ -9772,7 +9772,7 @@ - A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -9833,7 +9833,7 @@ - A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand. + 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 @@ -9885,7 +9885,7 @@ - A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -9923,7 +9923,7 @@ - An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. + 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 @@ -9969,7 +9969,7 @@ - A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. + A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. IEDB IEDB qualitative binding|purified MHC/direct/radioactivity @@ -10007,7 +10007,7 @@ - A flow cytometry assay that detects interleukin-8 production by T cells. + A flow cytometry assay that detects interleukin-8 production by T cells. IEDB IEDB IL-8 release|ICS @@ -10045,7 +10045,7 @@ - A cytometric bead array assay that detects interleukin-23 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 @@ -10114,7 +10114,7 @@ - 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. + 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 @@ -10201,7 +10201,7 @@ - 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. + 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 @@ -10253,7 +10253,7 @@ - A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro. + A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB histamine release|biological activity @@ -10287,7 +10287,7 @@ - A B cell epitope dependent biological activity determination assay that detects 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 @@ -10339,7 +10339,7 @@ - A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro . + A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro . PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB complement-dependent cytotoxicity|biological activity @@ -10391,7 +10391,7 @@ - A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro. + A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antibody-dependent cellular cytotoxicity|biological activity @@ -10425,7 +10425,7 @@ - A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. + 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 @@ -10477,7 +10477,7 @@ - A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro . + A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro . PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB opsonization|biological activity @@ -10509,7 +10509,7 @@ - A calorimetric binding assay that detects the binding of an antigen with an antibody. + 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 @@ -10541,7 +10541,7 @@ - An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex + 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 @@ -10573,7 +10573,7 @@ - A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex. + 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) @@ -10605,7 +10605,7 @@ - A cross-blocking assay that detects the binding of an antigen with an antibody. + 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 @@ -10637,7 +10637,7 @@ - A radio immuno assay that detects the binding of an antigen with an antibody. + 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) @@ -10669,7 +10669,7 @@ - An immunoblot assay that detects the binding of an antigen with an antibody. + 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 @@ -10701,7 +10701,7 @@ - A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody. + 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) @@ -10733,7 +10733,7 @@ - An immuno staining assay that detects the binding of an antigen with an antibody. + 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 @@ -10765,7 +10765,7 @@ - An immunoprecipitation assay that detects the binding of an antigen with an antibody. + An immunoprecipitation assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|immunoprecipitation @@ -10797,7 +10797,7 @@ - A mass spectrometry assay that detects the binding of an antigen with an antibody. + 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 @@ -10829,7 +10829,7 @@ - A phage display binding assay that detects the binding of an antigen with an antibody. + 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 @@ -10861,7 +10861,7 @@ - An electron microscopy imaging assay that detects the binding of an antigen with an antibody. + 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 @@ -10893,7 +10893,7 @@ - An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody. + 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 @@ -10925,7 +10925,7 @@ - An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody. + 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 @@ -10957,7 +10957,7 @@ - A flow cytometry assay that detects the binding of an antigen with an antibody. + A flow cytometry assay that detects the binding of an antigen with an antibody. IEDB IEDB qualitative binding|flow cytometry @@ -10995,7 +10995,7 @@ - A flow cytometry assay that detects epitope specific granzyme A release by T cells. + A flow cytometry assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|intracellular staining @@ -11027,7 +11027,7 @@ - An analytical chromatography assay that detects the binding of an antigen with an antibody. + 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 @@ -11070,7 +11070,7 @@ - A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. + 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) @@ -11108,7 +11108,7 @@ - An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. + An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|ELISA @@ -11146,7 +11146,7 @@ - A flow cytometry assay that detects epitope specific granulysin release by T cells. + A flow cytometry assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|intracellular staining @@ -11201,7 +11201,7 @@ - A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -11256,7 +11256,7 @@ - A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand. + 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 @@ -11325,7 +11325,7 @@ - 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. + 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 @@ -11363,7 +11363,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. + An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. IEDB IEDB IL-17A release|ELISA @@ -11401,7 +11401,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells. + 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 @@ -11456,7 +11456,7 @@ - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of 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 @@ -11518,7 +11518,7 @@ - An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. + 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 @@ -11580,7 +11580,7 @@ - An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. + 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 @@ -11632,7 +11632,7 @@ - A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro. + A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB agglutination|biological activity @@ -11708,7 +11708,7 @@ - An in vivo assay measuring B cell epitope specific protection from other challenge using survival. + An in vivo assay measuring B cell epitope specific protection from other challenge using survival. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB survival from challenge|in vivo assay @@ -11769,7 +11769,7 @@ - An efficacy of B cell epitope intervention experiment that detects a decrease in 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 @@ -11826,7 +11826,7 @@ - A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. + 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 @@ -11884,7 +11884,7 @@ - A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. + 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 @@ -11922,7 +11922,7 @@ - An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output. + 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 @@ -11969,7 +11969,7 @@ - A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. + A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. IEDB IEDB secondary in vitro activity|biological activity @@ -12014,7 +12014,7 @@ - A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. + 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 @@ -12047,7 +12047,7 @@ - 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. + 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 @@ -12088,7 +12088,7 @@ - A B cell epitope binding constant determination assay that measures the dissociation constant KD. + 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 @@ -12120,7 +12120,7 @@ - A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. + 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 @@ -12177,7 +12177,7 @@ - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. + 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 @@ -12234,7 +12234,7 @@ - An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. + 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 @@ -12275,7 +12275,7 @@ - A B cell epitope binding constant determination assay that measures the on rate. + 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 @@ -12316,7 +12316,7 @@ - A B cell epitope binding constant determination assay that measures the association constant KA. + 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 @@ -12348,7 +12348,7 @@ - A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody 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 @@ -12389,7 +12389,7 @@ - A B cell epitope binding constant determination assay that measures the off rate. + 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 @@ -12421,7 +12421,7 @@ - A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody. + 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 @@ -12453,7 +12453,7 @@ - A fluorescence quenching assay that detects the binding of an antigen with an antibody. + 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 @@ -12494,7 +12494,7 @@ - A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + 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 @@ -12535,7 +12535,7 @@ - An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + 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 @@ -12576,7 +12576,7 @@ - A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + 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 @@ -12617,7 +12617,7 @@ - A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody. + 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 @@ -12658,7 +12658,7 @@ - A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + 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 @@ -12699,7 +12699,7 @@ - A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody. + 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 @@ -12740,7 +12740,7 @@ - A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody. + 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 @@ -12781,7 +12781,7 @@ - A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + 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 @@ -12822,7 +12822,7 @@ - An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody. + 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 @@ -12863,7 +12863,7 @@ - A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody. + 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 @@ -12904,7 +12904,7 @@ - A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex. + 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 @@ -12945,7 +12945,7 @@ - A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody. + 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 @@ -12986,7 +12986,7 @@ - A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody. + 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 @@ -13027,7 +13027,7 @@ - A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody. + 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 @@ -13068,7 +13068,7 @@ - A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody. + 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 @@ -13106,7 +13106,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells. + 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 @@ -13144,7 +13144,7 @@ - A flow cytometry assay that detects interleukin-1 alpha production by T cells. + 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 @@ -13182,7 +13182,7 @@ - An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells. + 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 @@ -13220,7 +13220,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells. + 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 @@ -13258,7 +13258,7 @@ - A cytometric bead array assay that detects interleukin-1 alpha production by T cells. + 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 @@ -13296,7 +13296,7 @@ - An enzyme-linked immunospot assay that detects interferon-beta production by T cells. + An enzyme-linked immunospot assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ELISPOT @@ -13334,7 +13334,7 @@ - A flow cytometry assay that detects interferon-beta production by T cells. + A flow cytometry assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ICS @@ -13372,7 +13372,7 @@ - A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells. + 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 @@ -13410,7 +13410,7 @@ - An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. + An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ELISA @@ -13448,7 +13448,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells. + 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 @@ -13486,7 +13486,7 @@ - An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells. + 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 @@ -13524,7 +13524,7 @@ - A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + 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 @@ -13562,7 +13562,7 @@ - An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + 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 @@ -13600,7 +13600,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells. + 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 @@ -13638,7 +13638,7 @@ - An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB IEDB CCL4/MIP-1b release|ELISPOT @@ -13676,7 +13676,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells. + 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 @@ -13714,7 +13714,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells. + 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 @@ -13752,7 +13752,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells. + 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 @@ -13790,7 +13790,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells. + 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 @@ -13828,7 +13828,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells. + 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 @@ -13866,7 +13866,7 @@ - A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells. + 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 @@ -13904,7 +13904,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells. + 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 @@ -13942,7 +13942,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells. + 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 @@ -13980,7 +13980,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells. + 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 @@ -14018,7 +14018,7 @@ - A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells. + 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 @@ -14056,7 +14056,7 @@ - A flow cytometry assay that detects vascular endothelial growth factor production by T cells. + A flow cytometry assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|ICS @@ -14094,7 +14094,7 @@ - An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. + An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|ELISPOT @@ -14132,7 +14132,7 @@ - An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. + 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 @@ -14170,7 +14170,7 @@ - An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. + 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 @@ -14208,7 +14208,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -14246,7 +14246,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -14284,7 +14284,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -14322,7 +14322,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -14360,7 +14360,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -14398,7 +14398,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -14436,7 +14436,7 @@ - An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells. + 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 @@ -14474,7 +14474,7 @@ - A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells. + 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 @@ -14512,7 +14512,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells. + 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 @@ -14550,7 +14550,7 @@ - A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells. + 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 @@ -14588,7 +14588,7 @@ - An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells. + 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 @@ -14626,7 +14626,7 @@ - A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells. + 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 @@ -14664,7 +14664,7 @@ - An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells. + 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 @@ -14702,7 +14702,7 @@ - A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. + A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|cytometric bead array @@ -14740,7 +14740,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells. + 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 @@ -14778,7 +14778,7 @@ - A flow cytometry assay that detects RANTES production by T cells. + A flow cytometry assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ICS @@ -14816,7 +14816,7 @@ - An enzyme-linked immunospot assay that detects RANTES production by T cells. + An enzyme-linked immunospot assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ELISPOT @@ -14854,7 +14854,7 @@ - An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. + An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. IEDB IEDB lymphotoxin A/TNFb release|ELISPOT @@ -14892,7 +14892,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells. + 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 @@ -14930,7 +14930,7 @@ - A cytometric bead array assay that detects lymphotoxin A production by T cells. + A cytometric bead array assay that detects lymphotoxin A production by T cells. IEDB IEDB lymphotoxin A/TNFb release|cytometric bead array @@ -14968,7 +14968,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells. + 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 @@ -15006,7 +15006,7 @@ - An enzyme-linked immunospot assay that detects IP-10 production by T cells. + 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 @@ -15044,7 +15044,7 @@ - A flow cytometry assay that detects IP-10 production by T cells. + 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 @@ -15082,7 +15082,7 @@ - An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. + An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|ELISPOT @@ -15120,7 +15120,7 @@ - A flow cytometry assay that detects interleukin-9 production by T cells. + A flow cytometry assay that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|ICS @@ -15158,7 +15158,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells. + 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 @@ -15196,7 +15196,7 @@ - An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. + An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. IEDB IEDB IL-8 release|ELISPOT @@ -15234,7 +15234,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells. + 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 @@ -15272,7 +15272,7 @@ - An enzyme-linked immunospot assay that detects interleukin-3 production by T cells. + 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 @@ -15310,7 +15310,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells. + 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 @@ -15348,7 +15348,7 @@ - An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. + An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|ELISPOT @@ -15386,7 +15386,7 @@ - A flow cytometry assay that detects interleukin-7 production by T cells. + A flow cytometry assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|ICS @@ -15424,7 +15424,7 @@ - A flow cytometry assay that detects interleukin-27 production by T cells. + A flow cytometry assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ICS @@ -15462,7 +15462,7 @@ - A cytometric bead array assay that detects interleukin-3 production by T cells. + 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 @@ -15500,7 +15500,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells. + 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 @@ -15538,7 +15538,7 @@ - A T cell epitope specific cytotoxic T cell degranulation assay that detects 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 @@ -15576,7 +15576,7 @@ - A T cell epitope specific cytotoxic T cell degranulation assay that detects 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 @@ -15614,7 +15614,7 @@ - A cytometric bead array assay that detects interleukin-27 production by T cells. + 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 @@ -15652,7 +15652,7 @@ - A flow cytometry assay that detects interleukin-23 production by T cells. + A flow cytometry assay that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ICS @@ -15690,7 +15690,7 @@ - An enzyme-linked immunospot assay that detects interleukin-27 production by T cells. + 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 @@ -15728,7 +15728,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells. + 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 @@ -15766,7 +15766,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells. + 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 @@ -15804,7 +15804,7 @@ - An enzyme-linked immunospot assay that detects interleukin-18 production by T cells. + 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 @@ -15842,7 +15842,7 @@ - An enzyme-linked immunospot assay that detects interleukin-22 production by T cells. + 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 @@ -15880,7 +15880,7 @@ - An enzyme-linked immunospot assay that detects interleukin-23 production by T cells. + 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 @@ -15918,7 +15918,7 @@ - A flow cytometry assay that detects interleukin-18 production by T cells. + A flow cytometry assay that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|ICS @@ -15956,7 +15956,7 @@ - An enzyme-linked immunospot assay that detects interleukin-21 production by T cells. + 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 @@ -15994,7 +15994,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells. + 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 @@ -16032,7 +16032,7 @@ - A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells. + 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 @@ -16070,7 +16070,7 @@ - An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells. + 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 @@ -16108,7 +16108,7 @@ - An enzyme-linked immunospot assay that detects interleukin-17F production by T cells. + 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 @@ -16146,7 +16146,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells. + 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 @@ -16184,7 +16184,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells. + 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 @@ -16222,7 +16222,7 @@ - An enzyme-linked immunospot assay that detects interleukin-17A production by T cells. + 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 @@ -16260,7 +16260,7 @@ - A cytometric bead array assay that detects interleukin-18 production by T cells. + 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 @@ -16298,7 +16298,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells. + 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 @@ -16336,7 +16336,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells. + 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 @@ -16374,7 +16374,7 @@ - An enzyme-linked immunospot assay that detects interleukin-16 production by T cells. + 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 @@ -16412,7 +16412,7 @@ - A flow cytometry assay that detects interleukin-16 production by T cells. + A flow cytometry assay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ICS @@ -16450,7 +16450,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells. + 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 @@ -16488,7 +16488,7 @@ - A flow cytometry assay that detects interleukin-1 beta production by T cells. + 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 @@ -16526,7 +16526,7 @@ - An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. + An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. IEDB IEDB IL-1b release|ELISPOT @@ -16564,7 +16564,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells. + 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 @@ -16602,7 +16602,7 @@ - An enzyme-linked immunospot assay that detects interleukin-12 production by T cells. + 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 @@ -16640,7 +16640,7 @@ - A flow cytometry assay that detects interleukin-15 production by T cells. + A flow cytometry assay that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ICS @@ -16678,7 +16678,7 @@ - An enzyme-linked immunospot assay that detects interleukin-15 production by T cells. + 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 @@ -16755,7 +16755,7 @@ - A MHC binding constant determination assay measuring equilibrium association constant (KA). + A MHC binding constant determination assay measuring equilibrium association constant (KA). IEDB IEDB association constant KA|binding assay|1/M @@ -16796,7 +16796,7 @@ - A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). + A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). IEDB IEDB dissociation constant KD|binding assay|nM @@ -16865,7 +16865,7 @@ - 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. + 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 @@ -16897,7 +16897,7 @@ - A MHC binding constant determination assay measuring half life of binding. + A MHC binding constant determination assay measuring half life of binding. IEDB IEDB half life|binding assay|min @@ -16938,7 +16938,7 @@ - A MHC binding constant determination assay measuring half maximal effective concentration (EC50). + A MHC binding constant determination assay measuring half maximal effective concentration (EC50). IEDB IEDB half maximal effective concentration (EC50)|binding assay|nM @@ -16970,7 +16970,7 @@ - A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). + A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). IEDB IEDB half maximal inhibitory concentration (IC50)|binding assay|nM @@ -17011,7 +17011,7 @@ - A MHC binding constant determination assay measuring binding off rate measurement data item (koff). + A MHC binding constant determination assay measuring binding off rate measurement data item (koff). IEDB IEDB off rate|binding assay|1/s @@ -17043,7 +17043,7 @@ - A MHC binding constant determination assay measuring binding on rate (kon). + A MHC binding constant determination assay measuring binding on rate (kon). IEDB IEDB on rate|binding assay|nM^-1s^-1 @@ -17084,7 +17084,7 @@ - An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody. + 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 @@ -17125,7 +17125,7 @@ - An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + 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 @@ -17157,7 +17157,7 @@ - A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody. + 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 @@ -17189,7 +17189,7 @@ - A immunohistochemistry assay that detects the binding of an antigen with an antibody. + A immunohistochemistry assay that detects the binding of an antigen with an antibody. IEDB IEDB qualitative binding|immunohistochemistry @@ -17221,7 +17221,7 @@ - A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure 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 @@ -17253,7 +17253,7 @@ - A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure 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 @@ -17318,7 +17318,7 @@ - An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay @@ -17383,7 +17383,7 @@ - An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden. + An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay @@ -17415,7 +17415,7 @@ - A microarray assay that detects the binding of an antigen with an antibody. + A microarray assay that detects the binding of an antigen with an antibody. IEDB IEDB qualitative binding|microarray @@ -17467,7 +17467,7 @@ - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. + 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 @@ -17500,7 +17500,7 @@ - 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. + 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 @@ -17538,7 +17538,7 @@ - A T cell epitope specific cytokine production assay that detects production of 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 @@ -17576,7 +17576,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -17614,7 +17614,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -17646,7 +17646,7 @@ - A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. + 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 @@ -17684,7 +17684,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells. + 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 @@ -17722,7 +17722,7 @@ - A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells. + 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 @@ -17774,7 +17774,7 @@ - An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. + An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. IEDB IEDB cytotoxicity|in vitro assay @@ -17812,7 +17812,7 @@ - A cytometric bead array assay that detects epitope specific granzyme A release by T cells. + A cytometric bead array assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|cytometric bead array @@ -17850,7 +17850,7 @@ - A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|RNA/DNA detection @@ -17888,7 +17888,7 @@ - A cytometric bead array assay that detects epitope specific granzyme B release by T cells. + A cytometric bead array assay that detects epitope specific granzyme B release by T cells. IEDB IEDB granzyme B release|cytometric bead array @@ -17926,7 +17926,7 @@ - A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells IEDB IEDB granzyme B release|RNA/DNA detection @@ -17964,7 +17964,7 @@ - A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. + A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. IEDB IEDB MIF release|cytometric bead array @@ -18002,7 +18002,7 @@ - A cytometric bead array assay that detects oncostatin M production by T cells. + A cytometric bead array assay that detects oncostatin M production by T cells. IEDB IEDB oncostatin M release|cytometric bead array @@ -18040,7 +18040,7 @@ - An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. + An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|ELISPOT @@ -18102,7 +18102,7 @@ - A T cell epitope specific proliferation assay that is performed in vivo. + A T cell epitope specific proliferation assay that is performed in vivo. IEDB IEDB proliferation|in vivo assay @@ -18154,7 +18154,7 @@ - A T cell epitope specific proliferation assay that is performed on cells in vitro. + A T cell epitope specific proliferation assay that is performed on cells in vitro. IEDB IEDB proliferation|in vitro assay @@ -18186,7 +18186,7 @@ - An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output. + 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 @@ -18243,7 +18243,7 @@ - An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. + An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. IEDB IEDB protection from challenge|in vivo assay @@ -18288,7 +18288,7 @@ - T cell epitope dependent biological activity assay that detects suppression of an in vitro response. + 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 @@ -18323,7 +18323,7 @@ - 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. + 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 @@ -18375,7 +18375,7 @@ - A CFSE assay that detects T cell epitope specific proliferation in vitro. + A CFSE assay that detects T cell epitope specific proliferation in vitro. IEDB IEDB proliferation|CFSE @@ -18416,7 +18416,7 @@ - A T cell epitope binding constant determination assay that measures the dissociation constant KD. + 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 @@ -18457,7 +18457,7 @@ - A T cell epitope binding constant determination assay that measures the on rate. + 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 @@ -18498,7 +18498,7 @@ - A T cell epitope binding constant determination assay that measures the off rate. + 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 @@ -18539,7 +18539,7 @@ - A T cell epitope binding constant determination assay that measures the association constant KA. + 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 @@ -18571,7 +18571,7 @@ - A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex + 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 @@ -18612,7 +18612,7 @@ - A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. + 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 @@ -18653,7 +18653,7 @@ - A bio-layer interferometry assay that measures the off rate of an antigen with an antibody. + 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 @@ -18685,7 +18685,7 @@ - A bio-layer interferometry assay that detects the binding of an antigen with an antibody. + 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 @@ -18726,7 +18726,7 @@ - A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. + 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 @@ -18782,7 +18782,7 @@ - A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells. + 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 @@ -18820,7 +18820,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -18864,7 +18864,7 @@ - A footprinting assay that detects the binding of an antigen with an antibody. + 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 @@ -18896,7 +18896,7 @@ - A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody. + 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 @@ -18934,7 +18934,7 @@ - An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. + An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNa release|ELISA @@ -18972,7 +18972,7 @@ - A T cell epitope specific cytokine production assay that detects 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 @@ -19033,7 +19033,7 @@ - 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. + 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 @@ -19101,7 +19101,7 @@ - An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic 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 @@ -19169,7 +19169,7 @@ - An efficacy of B cell epitope intervention experiment that detects a decrease in disease after 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 @@ -19230,7 +19230,7 @@ - An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic 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 @@ -19291,7 +19291,7 @@ - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after 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 @@ -19365,7 +19365,7 @@ - An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. IEDB IEDB pathogen burden after challenge after adoptive transfer|in vivo assay @@ -19439,7 +19439,7 @@ - An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. IEDB IEDB pathogen burden after challenge after adoptive transfer|in vivo assay @@ -19524,7 +19524,7 @@ - An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival. + An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB survival from other challenge after adoptive transfer|in vivo assay @@ -19609,7 +19609,7 @@ - An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB survival from other challenge after adoptive transfer|in vivo assay @@ -19683,7 +19683,7 @@ - An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden. + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden. IEDB IEDB tumor burden after challenge after adoptive transfer|in vivo assay @@ -19757,7 +19757,7 @@ - An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden. + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden. IEDB IEDB tumor burden after challenge after adoptive transfer|in vivo assay @@ -19823,7 +19823,7 @@ - An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic 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 @@ -19889,7 +19889,7 @@ - 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. + 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 @@ -19927,7 +19927,7 @@ - A cytometric bead array assay that detects interleukin-15 production by T cells. + A cytometric bead array assay that detects interleukin-15 production by T cells. IEDB IEDB IL-15 release|cytometric bead array @@ -19965,7 +19965,7 @@ - A cytometric bead array assay that detects interleukin-16 production by T cells. + A cytometric bead array assay that detects interleukin-16 production by T cells. IEDB IEDB IL-16 release|cytometric bead array @@ -20031,7 +20031,7 @@ - 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. + 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 @@ -20097,7 +20097,7 @@ - An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic 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 @@ -20163,7 +20163,7 @@ - A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic 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 @@ -20229,7 +20229,7 @@ - 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. + 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|in vivo assay @@ -20295,7 +20295,7 @@ - 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. + 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|in vivo assay @@ -20361,7 +20361,7 @@ - An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells. + An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells. IEDB IEDB cytotoxicity after adoptive transfer|in vivo assay @@ -20399,7 +20399,7 @@ - An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. + An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|ELISA @@ -20460,7 +20460,7 @@ - An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic 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 @@ -20521,7 +20521,7 @@ - An efficacy of B cell epitope intervention experiment that is performed 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 @@ -20582,7 +20582,7 @@ - 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. + 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 @@ -20651,7 +20651,7 @@ - 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. + 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 @@ -20690,7 +20690,7 @@ - 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. + 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 @@ -20746,7 +20746,7 @@ - An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output. + 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 @@ -20778,7 +20778,7 @@ - An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output. + 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 @@ -20810,7 +20810,7 @@ - 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. + 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 @@ -20848,7 +20848,7 @@ - A cytometric bead array assay that detects epitope specific granulysin release by T cells. + A cytometric bead array assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|cytometric bead array @@ -20886,7 +20886,7 @@ - A cytometric bead array assay that detects epitope specific perforin release by T cells. + A cytometric bead array assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|cytometric bead array @@ -20924,7 +20924,7 @@ - A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. + A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. IEDB IEDB amphiregulin release|biological activity @@ -20962,7 +20962,7 @@ - An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. + An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. IEDB IEDB amphiregulin release|ELISA @@ -21000,7 +21000,7 @@ Next-generation high-density peptide microarrays measuring antibody responses to overlapping peptides: PMID:25922409. - A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. + A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. IEDB IEDB antibody binding|High throughput multiplexed assay @@ -21014,7 +21014,7 @@ Adaptive Biotech multiplexed TCR sequencing assays: PMID:32793919. - A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. + A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. IEDB IEDB T cell binding|High throughput multiplexed assay @@ -21028,7 +21028,7 @@ Peptide microarray with fluorescence detection for millions of MHC binding measurements: PMID: 33705522. - A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. + A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. IEDB IEDB MHC binding|High throughput multiplexed assay @@ -21042,7 +21042,7 @@ Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands witth a false discovery rate: PMID: 29789417. - A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. IEDB IEDB ligand presentation|High throughput multiplexed assay @@ -21086,7 +21086,7 @@ - A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells. + A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells. IEDB IEDB lymphotactin release|biological activity @@ -21124,7 +21124,7 @@ - An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells. + An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells. IEDB IEDB lymphotactin release|ELISA @@ -21219,7 +21219,7 @@ - An in vivo assay measuring T cell epitope specific protection from pathogen challenge. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge. IEDB IEDB protection from pathogen challenge|in vivo assay @@ -21284,7 +21284,7 @@ - An in vivo assay measuring T cell epitope specific protection from tumor challenge. + An in vivo assay measuring T cell epitope specific protection from tumor challenge. IEDB IEDB protection from tumor challenge|in vivo assay @@ -21360,7 +21360,7 @@ - An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor. + An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor. IEDB IEDB protection from other challenge|in vivo assay @@ -21425,7 +21425,7 @@ - An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival. + An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival. IEDB IEDB survival from tumor challenge|in vivo assay @@ -21490,7 +21490,7 @@ - An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival. IEDB IEDB survival from pathogen challenge|in vivo assay @@ -21555,7 +21555,7 @@ - An in vivo assay measuring B cell epitope specific protection from pathogen challenge. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge. IEDB IEDB protection from pathogen challenge|in vivo assay @@ -21620,7 +21620,7 @@ - An in vivo assay measuring B cell epitope specific protection from tumor challenge. + An in vivo assay measuring B cell epitope specific protection from tumor challenge. IEDB IEDB protection from tumor challenge|in vivo assay @@ -21696,7 +21696,7 @@ - An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor. + An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor. IEDB IEDB protection from other challenge|in vivo assay @@ -21761,7 +21761,7 @@ - An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival. IEDB IEDB survival from pathogen challenge|in vivo assay @@ -21826,7 +21826,7 @@ - An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival. + An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival. IEDB IEDB survival from tumor challenge|in vivo assay @@ -21891,7 +21891,7 @@ - An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from pathogen challenge after adoptive transfer|in vivo assay @@ -21965,7 +21965,7 @@ - An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB survival after pathogen challenge after adoptive transfer|in vivo assay @@ -22030,7 +22030,7 @@ - An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells. + An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells. IEDB IEDB protection from tumor challenge after adoptive transfer|in vivo assay @@ -22104,7 +22104,7 @@ - An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival. + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB survival after tumor challenge after adoptive transfer|in vivo assay @@ -22180,7 +22180,7 @@ - An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells. + An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells. IEDB IEDB protection from other challenge after adoptive transfer|in vivo assay @@ -22245,7 +22245,7 @@ - An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from pathogen challenge after adoptive transfer|in vivo assay @@ -22319,7 +22319,7 @@ - An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB survival after pathogen challenge after adoptive transfer|in vivo assay @@ -22384,7 +22384,7 @@ - An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from tumor challenge after adoptive transfer|in vivo assay @@ -22458,7 +22458,7 @@ - An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB survival after tumor challenge after adoptive transfer|in vivo assay @@ -22534,7 +22534,7 @@ - An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from other challenge after adoptive transfer|in vivo assay @@ -22572,7 +22572,7 @@ - A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells. + A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|biological activity @@ -22610,7 +22610,7 @@ - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells. + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|RNA/DNA detection @@ -22648,7 +22648,7 @@ - A flow cytometry assay that detects interleukin-25 production by T cells. + A flow cytometry assay that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|ICS @@ -22686,7 +22686,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. + An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|ELISA @@ -22724,7 +22724,7 @@ - A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. + A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. IEDB IEDB TNF release|bioassay @@ -22772,7 +22772,7 @@ quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. Bjoern Peters Randi Vita Sebastian Duesing @@ -22807,7 +22807,7 @@ - An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex. + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex. PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters IEDB 3D structure|electron microscopy @@ -22839,7 +22839,7 @@ - An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex. + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex. PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters IEDB 3D structure|electron microscopy @@ -22889,7 +22889,7 @@ - An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. + 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 @@ -22921,7 +22921,7 @@ - A T cell epitope assay that measures the binding of T cell receptor to an epitope. + A T cell epitope assay that measures the binding of T cell receptor to an epitope. IEDB IEDB T cell binding|any method @@ -22965,7 +22965,7 @@ - An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. + An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|ELISPOT @@ -22997,7 +22997,7 @@ - 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. + 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 @@ -23049,7 +23049,7 @@ - A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. + 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 @@ -23081,7 +23081,7 @@ - A MHC ligand assay that detects the binding of a ligand to an MHC molecule. + A MHC ligand assay that detects the binding of a ligand to an MHC molecule. IEDB IEDB MHC binding|any method @@ -23113,7 +23113,7 @@ - A B cell epitope assay that measures the binding of an antibody receptor to an epitope. + A B cell epitope assay that measures the binding of an antibody receptor to an epitope. IEDB IEDB antibody binding|any method @@ -23172,7 +23172,7 @@ - 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. + 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 @@ -23210,7 +23210,7 @@ - A T cell epitope assay that detects cytokine production by T cells. + A T cell epitope assay that detects cytokine production by T cells. IEDB IEDB cytokine release|biological activity @@ -23248,7 +23248,7 @@ - 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. + 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 @@ -23286,7 +23286,7 @@ - A T cell epitope dependent biological activity assay that detects T cell proliferation. + A T cell epitope dependent biological activity assay that detects T cell proliferation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB proliferation|biological activity @@ -23338,7 +23338,7 @@ - A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. + A chromium release 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|51 chromium @@ -23376,7 +23376,7 @@ - An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. + An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|ELISA @@ -23414,7 +23414,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. + 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 @@ -23452,7 +23452,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. + 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 @@ -23490,7 +23490,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. + 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 @@ -23528,7 +23528,7 @@ - An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells. + An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|ELISA @@ -23566,7 +23566,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells. + 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 @@ -23604,7 +23604,7 @@ - An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells. + 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 @@ -23642,7 +23642,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells. + 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 @@ -23680,7 +23680,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells. + 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 @@ -23718,7 +23718,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells. + 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 @@ -23756,7 +23756,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells. + 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 @@ -23794,7 +23794,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. + 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 @@ -23832,7 +23832,7 @@ - An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. + 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 @@ -23870,7 +23870,7 @@ - An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. + 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 @@ -23908,7 +23908,7 @@ - An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells + An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells IEDB IEDB TNFa release|ELISPOT @@ -23946,7 +23946,7 @@ - An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. + 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 @@ -23984,7 +23984,7 @@ - An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. + 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 @@ -24022,7 +24022,7 @@ - A flow cytometry assay that detects interferon-gamma production by T cells. + A flow cytometry assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|ICS @@ -24060,7 +24060,7 @@ - A flow cytometry assay that detects interleukin-2 production by T cells. + A flow cytometry assay that detects interleukin-2 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|ICS @@ -24098,7 +24098,7 @@ - A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. + A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|ICS @@ -24136,7 +24136,7 @@ - A flow cytometry assay that detects interleukin-4 production by T cells. + A flow cytometry assay that detects interleukin-4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|ICS @@ -24174,7 +24174,7 @@ - A flow cytometry assay that detects interleukin-10 production by T cells. + A flow cytometry assay that detects interleukin-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|ICS @@ -24212,7 +24212,7 @@ - A flow cytometry assay that detects interleukin-17 production by T cells. + A flow cytometry assay that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|ICS @@ -24266,7 +24266,7 @@ - A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. + 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 @@ -24318,7 +24318,7 @@ - A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro. + A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro. IEDB IEDB proliferation|3H-thymidine @@ -24370,7 +24370,7 @@ - A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro. + A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro. IEDB IEDB proliferation|BrdU diff --git a/src/ontology/modules/medical-history.owl b/src/ontology/modules/medical-history.owl index 8d4bf194..a3f717cf 100644 --- a/src/ontology/modules/medical-history.owl +++ b/src/ontology/modules/medical-history.owl @@ -97,7 +97,7 @@ - A clinical history in which there is a diagnosis of cancer. + A clinical history in which there is a diagnosis of cancer. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -110,7 +110,7 @@ - A clinical history in which there was no diagnosis 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 @@ -124,7 +124,7 @@ - A clinical history in which it is not known whether there was a diagnosis 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 @@ -137,7 +137,7 @@ - A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has 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 @@ -151,7 +151,7 @@ - A clinical history in which there is a diagnosis of cancer in a blood relative. + 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 @@ -165,7 +165,7 @@ - A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. + 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 @@ -178,7 +178,7 @@ - A clinical history in which there is a diagnosis of cancer in a male sibling. + A clinical history in which there is a diagnosis of cancer in a male sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -191,7 +191,7 @@ - A clinical history in which there is a diagnosis of cancer in a person's female child. + A clinical history in which there is a diagnosis of cancer in a person's female child. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -204,7 +204,7 @@ - A clinical history in which there is a diagnosis of cancer in a male parent. + A clinical history in which there is a diagnosis of cancer in a male parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -217,7 +217,7 @@ - A clinical history in which there is a diagnosis of cancer in a female parent. + A clinical history in which there is a diagnosis of cancer in a female parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -230,7 +230,7 @@ - A clinical history in which there is a diagnosis of cancer in a female sibling. + A clinical history in which there is a diagnosis of cancer in a female sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -243,7 +243,7 @@ - A clinical history in which there is a diagnosis of cancer in a person's male child. + A clinical history in which there is a diagnosis of cancer in a person's male child. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -256,7 +256,7 @@ - A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. + 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 @@ -269,7 +269,7 @@ - A clinical history in which there is a diagnosis of cancer in a female parent of a parent. + 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 @@ -282,7 +282,7 @@ - A clinical history in which there is a diagnosis of cancer in a male parent of a parent. + 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 @@ -295,7 +295,7 @@ - A clinical history in which there is a diagnosis of cancer in a male child of a sibling. + 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 @@ -308,7 +308,7 @@ - A clinical history in which there is a diagnosis of cancer in a female child of a sibling. + 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 @@ -321,7 +321,7 @@ - A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an 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 @@ -334,7 +334,7 @@ - A diagnosis of infectious disease caused by the hepatitis B virus. + A diagnosis of infectious disease caused by the hepatitis B virus. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -347,7 +347,7 @@ - A diagnosis of infectious disease caused by the hepatitis C virus. + A diagnosis of infectious disease caused by the hepatitis C virus. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -360,7 +360,7 @@ - A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). + A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -373,7 +373,7 @@ - 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. + 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 @@ -386,7 +386,7 @@ - A clinical history in which there has been second hand exposure to tobacco smoking. + A clinical history in which there has been second hand exposure to tobacco smoking. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -399,7 +399,7 @@ - An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. + 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 @@ -412,7 +412,7 @@ - An exposure to second hand smoke in person's current household. + An exposure to second hand smoke in person's current household. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -425,7 +425,7 @@ - A clinical history in which a female has had a pregnancy. + A clinical history in which a female has had a pregnancy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -438,7 +438,7 @@ - A measurement datum of the total number of pregnancies a woman has had. + A measurement datum of the total number of pregnancies a woman has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -451,7 +451,7 @@ - A measurement datum of the total number of live births a female has had. + A measurement datum of the total number of live births a female has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -464,7 +464,7 @@ - An age measurement datum performed on a female when her first biological child was born. + An age measurement datum performed on a female when her first biological child was born. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -477,7 +477,7 @@ - A clinical history in which a woman has had gynecologic surgery in the past. + A clinical history in which a woman has had gynecologic surgery in the past. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -490,7 +490,7 @@ - A gynecologic surgery history in which a woman has had a hysterectomy. + A gynecologic surgery history in which a woman has had a hysterectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -503,7 +503,7 @@ - A gynecologic surgery history in which a woman has had a unilateral oophorectomy. + A gynecologic surgery history in which a woman has had a unilateral oophorectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -516,7 +516,7 @@ - A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. + 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 @@ -529,7 +529,7 @@ - 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. + 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 @@ -542,7 +542,7 @@ - A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. + 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 @@ -555,7 +555,7 @@ - A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. + 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 @@ -568,7 +568,7 @@ - A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. + 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 @@ -581,7 +581,7 @@ - A clinical history in which an individual has had hormonal replacement therapy in the past. + A clinical history in which an individual has had hormonal replacement therapy in the past. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -594,7 +594,7 @@ - A processed material used for delivery of hormones in hormone 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 @@ -608,7 +608,7 @@ - A delivery form for hormonal replacement therapy that is a pill for oral administration. + A delivery form for hormonal replacement therapy that is a pill for oral administration. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -621,7 +621,7 @@ - A delivery form for hormonal replacement therapy that is a patch for transdermal administration. + A delivery form for hormonal replacement therapy that is a patch for transdermal administration. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -634,7 +634,7 @@ - A delivery form for hormonal replacement therapy that is a cream for transdermal administration. + A delivery form for hormonal replacement therapy that is a cream for transdermal administration. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -647,7 +647,7 @@ - An information content entity that indicates the state of a female's cessation of menstruation. + An information content entity that indicates the state of a female's cessation of menstruation. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -660,7 +660,7 @@ - A menopausal status that is neither pre- nor post-menopausal. + A menopausal status that is neither pre- nor post-menopausal. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -673,7 +673,7 @@ - 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. + 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 @@ -686,7 +686,7 @@ - A menopausal status indicating that it has been 6-12 months since last menstrual period. + A menopausal status indicating that it has been 6-12 months since last menstrual period. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -699,7 +699,7 @@ - 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. + 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 @@ -712,7 +712,7 @@ - An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -725,7 +725,7 @@ - An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. + An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -738,7 +738,7 @@ - An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. + An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -751,7 +751,7 @@ - An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. + An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -764,7 +764,7 @@ - An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. + An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -777,7 +777,7 @@ - An exposure to environmental and workplace carcinogens history where the carcinogen is silica. + An exposure to environmental and workplace carcinogens history where the carcinogen is silica. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -790,7 +790,7 @@ - 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. + 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 @@ -804,7 +804,7 @@ - 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. + 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 @@ -818,7 +818,7 @@ - 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. + 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 @@ -831,7 +831,7 @@ - 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 + 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 @@ -844,7 +844,7 @@ - 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 + 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 @@ -858,7 +858,7 @@ 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. + 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 @@ -872,7 +872,7 @@ 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. + 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 @@ -886,7 +886,7 @@ 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. + 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 @@ -900,7 +900,7 @@ 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. + 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 @@ -913,7 +913,7 @@ - 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. + 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 @@ -927,7 +927,7 @@ 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. + 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 @@ -941,7 +941,7 @@ 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. + 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 @@ -955,7 +955,7 @@ 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. + 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 @@ -968,7 +968,7 @@ - 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. + 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 @@ -982,7 +982,7 @@ 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. + 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 diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index d1a15197..3aeb9954 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -110,7 +110,7 @@ - A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. + 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 @@ -126,7 +126,7 @@ 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 + 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 @@ -143,7 +143,7 @@ 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. + 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 @@ -158,7 +158,7 @@ - Label role is a role which inheres in a material entity and which is realized in a detection of label assay + 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 @@ -176,7 +176,7 @@ 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. + 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 @@ -191,7 +191,7 @@ - a worker role of providing medical care either within or outside the study timeline + a worker role of providing medical care either within or outside the study timeline Person:Jennifer Fostel health care provider @@ -208,7 +208,7 @@ 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 + 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 @@ -223,7 +223,7 @@ - Place holder class, Utility class to gather the defined classes + Place holder class, Utility class to gather the defined classes Susanna Sansone OBI Biomaterial derived @@ -239,7 +239,7 @@ 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. + 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 @@ -257,7 +257,7 @@ 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 + 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 @@ -272,7 +272,7 @@ - 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 @@ -302,7 +302,7 @@ A trypsinized suspension of cells - A material entity that has undergone a process of digestion with trypsin + A material entity that has undergone a process of digestion with trypsin Person:Bjoern Peters obsolete_trypsinized material @@ -317,7 +317,7 @@ 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 + 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 @@ -333,7 +333,7 @@ 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 + 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 @@ -348,7 +348,7 @@ 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. + 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 @@ -365,7 +365,7 @@ 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. + 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. @@ -381,7 +381,7 @@ 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. + 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 @@ -401,7 +401,7 @@ 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 + 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 @@ -419,7 +419,7 @@ - Study result is an information content entity that is a specified data output of a study. + Study result is an information content entity that is a specified data output of a study. GROUP: OBI obsolete_study result @@ -433,7 +433,7 @@ - A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule + 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 @@ -464,7 +464,7 @@ 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 + 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 @@ -477,7 +477,7 @@ - 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 + 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 @@ -492,7 +492,7 @@ 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 + 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 @@ -521,7 +521,7 @@ - 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 @@ -548,7 +548,7 @@ 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 + a service provider role which is realized by a servicer provider organization performing some training PERSON:Helen Parkinson OBI @@ -564,7 +564,7 @@ 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 + a service provider role which is realized by a servicer provider organization performing access to some material PERSON:Helen Parkinson OBI @@ -601,7 +601,7 @@ - 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 @@ -626,7 +626,7 @@ 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 + a service provider role which is realized by a servicer provider organization performing a protocol execution PERSON:Helen Parkinson obsolete_protocol service provider role @@ -640,7 +640,7 @@ - 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 @@ -666,7 +666,7 @@ 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 + The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis https://github.com/obi-ontology/obi/issues/623 obsolete performing a diagnosis @@ -680,7 +680,7 @@ - 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. + 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 @@ -694,7 +694,7 @@ - A specimen fixation function is a function that holds or fastens an entity in a fixed position. + A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I obsolete_specimen fixation function @@ -708,7 +708,7 @@ - An intracellular material detection by flow cytometry assay that measures 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) @@ -726,7 +726,7 @@ 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 + An assay that identifies an MHC ligand using a T cell response assay as a readout PERSON: Randi Vita, Bjoern Peters IEDB @@ -743,7 +743,7 @@ - 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. + 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 @@ -758,7 +758,7 @@ - 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. + 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 @@ -773,7 +773,7 @@ - competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate + 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) @@ -790,7 +790,7 @@ - An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. + 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 @@ -805,7 +805,7 @@ - direct binding assay measuring MHC ligand binding using MHC derived from a cell + direct binding assay measuring MHC ligand binding using MHC derived from a cell PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) @@ -821,7 +821,7 @@ - direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation + 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) @@ -837,7 +837,7 @@ - A direct binding assay using a assay + A direct binding assay using a assay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) @@ -853,7 +853,7 @@ - A competitive inhibition of binding assay using a assay + A competitive inhibition of binding assay using a assay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) @@ -869,7 +869,7 @@ - A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms + A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) @@ -887,7 +887,7 @@ 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' + 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 @@ -905,7 +905,7 @@ a single Hela cell - a cell derived from a multicellular organism that has the potential to replicate indefinitely + a cell derived from a multicellular organism that has the potential to replicate indefinitely PERSON: Bjoern Peters GROUP: OBI Biomaterial Branch @@ -921,7 +921,7 @@ the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme - A material entity which is derived from a protein + A material entity which is derived from a protein PERSON: Bjoern Peters GROUP: IEDB @@ -936,7 +936,7 @@ - A material entity that represents generations of a primary culture. + A material entity that represents generations of a primary culture. PERSON: Susanna Sansone GROUP: OBI Biomaterial Branch @@ -951,7 +951,7 @@ - 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. PERSON:Matthew Brush immortal cell line sample permanent cell line @@ -971,7 +971,7 @@ 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). + 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) @@ -988,7 +988,7 @@ - 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. + 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 @@ -1005,7 +1005,7 @@ 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. + 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 @@ -1022,7 +1022,7 @@ 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 + a collection is a bfo:aggregate object, that is a set of material object of the same kind PERSON: Susanna Sansone ensemble group @@ -1041,7 +1041,7 @@ 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 + 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 @@ -1057,7 +1057,7 @@ 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. + 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 @@ -1073,7 +1073,7 @@ 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!) + 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 @@ -1088,7 +1088,7 @@ - A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. + 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 @@ -1105,7 +1105,7 @@ - Place holder class, see editor note + Place holder class, see editor note PlanAndPlannedProcess Branch OBI branch derived @@ -1120,7 +1120,7 @@ - An occurrence of disease is a process involving pathologic changes within an organism + An occurrence of disease is a process involving pathologic changes within an organism IEDB IEDB @@ -1135,7 +1135,7 @@ - placeholder to be imported from disease ontology + placeholder to be imported from disease ontology IEDB IEDB @@ -1150,7 +1150,7 @@ - A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. + A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. CD8 https://github.com/obi-ontology/obi/issues/353 @@ -1165,7 +1165,7 @@ - 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. + 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 @@ -1181,7 +1181,7 @@ - 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 + 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 diff --git a/src/ontology/modules/organizations.owl b/src/ontology/modules/organizations.owl index d424f7f6..b4cce305 100644 --- a/src/ontology/modules/organizations.owl +++ b/src/ontology/modules/organizations.owl @@ -123,7 +123,7 @@ Affymetrix Affymetrix supplied microarray - An organization which supplies technology, tools and protocols for use in high throughput applications + An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix @@ -505,7 +505,7 @@ Nimblegen - An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen @@ -517,7 +517,7 @@ 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. + 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 @@ -529,7 +529,7 @@ 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. + 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 @@ -540,7 +540,7 @@ 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. + 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 @@ -553,7 +553,7 @@ Oxford Nanopore Technologies - An organization that is developing and selling nanopore sequencing products and is based in the UK. + 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 @@ -566,7 +566,7 @@ BioGents - An organization that manufactures mosquito traps and other mosquito control products. + An organization that manufactures mosquito traps and other mosquito control products. John Judkins WEB:https://eu.biogents.com/about-biogents/ BioGents @@ -579,7 +579,7 @@ Abbott - A manufacturer of rapid point-of-care assay devices. + A manufacturer of rapid point-of-care assay devices. John Judkins ORCID:0000-0001-6595-0902 WEB:https://www.globalpointofcare.abbott/en/about.html https://github.com/obi-ontology/obi/issues/1456 @@ -593,7 +593,7 @@ J. Mitra - A manufacturer of in vitro diagnostic assay kits in India. + A manufacturer of in vitro diagnostic assay kits in India. John Judkins ORCID:0000-0001-6595-0902 WEB:https://jmitra.co.in/about-us/ https://github.com/obi-ontology/obi/issues/1456 @@ -607,7 +607,7 @@ InBios - A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. + A manufacturer that specializes in in vitro diagnostic devices designed to test for infectious diseases. John Judkins ORCID:0000-0001-6595-0902 WEB:https://inbios.com/about/ https://github.com/obi-ontology/obi/issues/1456 diff --git a/src/ontology/modules/physical-examination.owl b/src/ontology/modules/physical-examination.owl index c07186b4..0839b7c0 100644 --- a/src/ontology/modules/physical-examination.owl +++ b/src/ontology/modules/physical-examination.owl @@ -156,7 +156,7 @@ - A physical examination of an organism's ability to perform functional activities. + A physical examination of an organism's ability to perform functional activities. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -191,7 +191,7 @@ - An observational assessment of the loss of facial muscle tissue due to inactivity or disease. + An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -226,7 +226,7 @@ - An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. + An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -261,7 +261,7 @@ - A functional assessment of an individual's ability to cough forcefully. + A functional assessment of an individual's ability to cough forcefully. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -296,7 +296,7 @@ - A functional assessment of an individual's ability to understandably repeat spoken sentences. + A functional assessment of an individual's ability to understandably repeat spoken sentences. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -331,7 +331,7 @@ - A functional assessment of an individual's ability to touch index fingers together in front of the sternum without oscillation for a specified duration of time + A functional assessment of an individual's ability to touch index fingers together in front of the sternum without oscillation for a specified duration of time Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -366,7 +366,7 @@ - A functional assessment of an individual's ability to touch their own nose and then touch an examiners finger in front of them and then touch their own nose once more. + A functional assessment of an individual's ability to touch their own nose and then touch an examiners finger in front of them and then touch their own nose once more. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -401,7 +401,7 @@ - A functional assessment of an individual's ability to accurately touch a moving target with their finger and then touch their own chin a number of times in a row. + A functional assessment of an individual's ability to accurately touch a moving target with their finger and then touch their own chin a number of times in a row. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -436,7 +436,7 @@ - A functional assessment of an individual's ability to alternate the forearm between pronation and suppination as quickly as possible during a specified duration of time + A functional assessment of an individual's ability to alternate the forearm between pronation and suppination as quickly as possible during a specified duration of time Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -471,7 +471,7 @@ - A functional assessment of an individual's ability to touch their finger-tip to thumb as many times as possible during a specified duration of time. + A functional assessment of an individual's ability to touch their finger-tip to thumb as many times as possible during a specified duration of time. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -506,7 +506,7 @@ - A functional assessment of an individual's ability to slide their heel back and forth along their contralateral tibia from the patella to the ankle with the contralateral leg extended. + A functional assessment of an individual's ability to slide their heel back and forth along their contralateral tibia from the patella to the ankle with the contralateral leg extended. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -541,7 +541,7 @@ - A functional assessment of an individual's ability to tap their heel to the midpoint of the contralateral shin a number of times. + A functional assessment of an individual's ability to tap their heel to the midpoint of the contralateral shin a number of times. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -576,7 +576,7 @@ - An observational assesment of an individual's muscle tissue loss due to inactivity or disease. + An observational assesment of an individual's muscle tissue loss due to inactivity or disease. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -611,7 +611,7 @@ - A functional assessment of an individual's ability to perform muscle movement to overcome gravity or physical resistence. + A functional assessment of an individual's ability to perform muscle movement to overcome gravity or physical resistence. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -646,7 +646,7 @@ - A functional assessment of an individual's ability to sense vibration. + A functional assessment of an individual's ability to sense vibration. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -681,7 +681,7 @@ - A functional assessment of an individual's ability to sense the position of a finger or toe that has been manipulated by minimal random movements. + A functional assessment of an individual's ability to sense the position of a finger or toe that has been manipulated by minimal random movements. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -716,7 +716,7 @@ - A functional assessment of an individual's muscle contraction when a muscle is triggered by a signal from a muscle spindle in response to a stimulus applied to a specific trigger point on the body. + A functional assessment of an individual's muscle contraction when a muscle is triggered by a signal from a muscle spindle in response to a stimulus applied to a specific trigger point on the body. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -740,7 +740,7 @@ - The functional assessment of an individual's ability to maintain balance, posture or upright stability. + The functional assessment of an individual's ability to maintain balance, posture or upright stability. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -764,7 +764,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain unsupported posture while sitting over a given time period. + A limits of stability assessment designed to assess an individual's ability to maintain unsupported posture while sitting over a given time period. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -788,7 +788,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet 20 cm apart. + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet 20 cm apart. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -812,7 +812,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with their eyes closed. + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with their eyes closed. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -836,7 +836,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together. + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -860,7 +860,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together and eyes closed. + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together and eyes closed. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -884,7 +884,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet in tandem placement. + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet in tandem placement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -908,7 +908,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain a stable stance on one foot. + A limits of stability assessment designed to assess an individual's ability to maintain a stable stance on one foot. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -932,7 +932,7 @@ - A limits of stability assessment designed to assess an individual's ability to maintain balance while walking in a straight line placing steps in tandem. + A limits of stability assessment designed to assess an individual's ability to maintain balance while walking in a straight line placing steps in tandem. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -956,7 +956,7 @@ - A limits of stability assessment designed to assess an individual's manner or pattern of walking. + A limits of stability assessment designed to assess an individual's manner or pattern of walking. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -980,7 +980,7 @@ - A functional assessment of an individual's lower cranial nerve function via proxy of facial muscle performance. + A functional assessment of an individual's lower cranial nerve function via proxy of facial muscle performance. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1004,7 +1004,7 @@ - A functional assessment of an individual's ability to articulate spoken words. + A functional assessment of an individual's ability to articulate spoken words. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1028,7 +1028,7 @@ - A functional assessment of an individual's ability to coordinate limb movement. + A functional assessment of an individual's ability to coordinate limb movement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1052,7 +1052,7 @@ - A limb coordination assessment designed to assess an individual's ability to coordinate upper limb movement. + A limb coordination assessment designed to assess an individual's ability to coordinate upper limb movement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1076,7 +1076,7 @@ - A limb coordination assessment designed to assess an individual's ability to coordinate lower limb movement. + A limb coordination assessment designed to assess an individual's ability to coordinate lower limb movement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1100,7 +1100,7 @@ - A functional assesment of an individual's nerve performance. Specifically the nerves connecting the sensory and motor structures with the central nervous system. + A functional assesment of an individual's nerve performance. Specifically the nerves connecting the sensory and motor structures with the central nervous system. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1124,7 +1124,7 @@ - A functional assessment of an individual's ability to maintain upright body posture. + A functional assessment of an individual's ability to maintain upright body posture. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1159,7 +1159,7 @@ - A deep tendon reflex assessment of an individual's reaction to stimulus applied to a knee joint. + A deep tendon reflex assessment of an individual's reaction to stimulus applied to a knee joint. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1172,7 +1172,7 @@ - A physical examination of an organism through visual assesment. + A physical examination of an organism through visual assesment. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1207,7 +1207,7 @@ - A deep tendon reflex assessment of an individual's reaction to stimulus applied to an ankle joint. + A deep tendon reflex assessment of an individual's reaction to stimulus applied to an ankle joint. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1242,7 +1242,7 @@ - A deep tendon reflex assessment of an individual's reaction to stimulus applied to a tendon of biceps brachii. + A deep tendon reflex assessment of an individual's reaction to stimulus applied to a tendon of biceps brachii. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -1277,7 +1277,7 @@ - A deep tendon reflex assessment of an individual's reaction to stimulus applied to a brachioradialis. + A deep tendon reflex assessment of an individual's reaction to stimulus applied to a brachioradialis. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 diff --git a/src/ontology/modules/sample-collection.owl b/src/ontology/modules/sample-collection.owl index b62e6e6b..ffafea91 100644 --- a/src/ontology/modules/sample-collection.owl +++ b/src/ontology/modules/sample-collection.owl @@ -73,7 +73,7 @@ - A live arthropod specimen collection process in which the arthropods are in the adult stage. + A live arthropod specimen collection process in which the arthropods are in the adult stage. John Judkins collection of adults MIRO:30000052 @@ -87,7 +87,7 @@ - An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. + An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. John Judkins animal biting catch MIRO:30000012 @@ -101,7 +101,7 @@ - An animal-biting arthropod specimen collection by aspiration that occurs outside a building. + An animal-biting arthropod specimen collection by aspiration that occurs outside a building. John Judkins animal biting catch - outdoors MIRO:30000014 @@ -115,7 +115,7 @@ - An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. + An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. John Judkins aquatic environment catch MIRO:30000048 @@ -129,7 +129,7 @@ - An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. + An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. John Judkins animal shed resting catch MIRO:30000027 @@ -143,7 +143,7 @@ - An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. + 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 @@ -157,7 +157,7 @@ - An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. + 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 @@ -171,7 +171,7 @@ - An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. + 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 @@ -185,7 +185,7 @@ - A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. + 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 @@ -199,7 +199,7 @@ - A specimen collection process that has the objective of collecting arthropods as specimens. + A specimen collection process that has the objective of collecting arthropods as specimens. John Judkins collection of arthropods field population catch @@ -214,7 +214,7 @@ - An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. + An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. John Judkins man biting catch MIRO:30000017 @@ -228,7 +228,7 @@ - An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. + 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 @@ -242,7 +242,7 @@ - An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. + 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 @@ -256,7 +256,7 @@ - A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. + A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. John Judkins pyrethrum spray catch MIRO:30000023 @@ -270,7 +270,7 @@ - An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. + 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 @@ -284,7 +284,7 @@ - An arthropod specimen collection process meant to collect live specimens. + An arthropod specimen collection process meant to collect live specimens. John Judkins catch of live specimens MIRO:30000044 @@ -299,7 +299,7 @@ - An arthropod specimen collection process in which the arthropods are in the embryo stage. + An arthropod specimen collection process in which the arthropods are in the embryo stage. VEuPath collection of eggs MIRO:30000049 @@ -313,7 +313,7 @@ - An arthropod specimen collection process in which the arthropods are in the larval stage. + An arthropod specimen collection process in which the arthropods are in the larval stage. VEuPath collection of larvae MIRO:30000022 @@ -327,7 +327,7 @@ - An arthropod specimen collection process in which the arthropods are in the pupal stage. + An arthropod specimen collection process in which the arthropods are in the pupal stage. VEuPath collection of pupae MIRO:30000050 diff --git a/src/ontology/modules/sequence-analysis.owl b/src/ontology/modules/sequence-analysis.owl index af3f709a..3f7cac1d 100644 --- a/src/ontology/modules/sequence-analysis.owl +++ b/src/ontology/modules/sequence-analysis.owl @@ -126,7 +126,7 @@ - A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). + A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios adapter-sequence trimming @@ -138,7 +138,7 @@ - A data transformation in which data contained in 2 or more files are merged into a single file. + A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios file merge @@ -162,7 +162,7 @@ - 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. + 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 @@ -186,7 +186,7 @@ - The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. + 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 @@ -208,7 +208,7 @@ - The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. + 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 @@ -220,7 +220,7 @@ - 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. + 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 @@ -232,7 +232,7 @@ - The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. + 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 @@ -244,7 +244,7 @@ - The results of a sequence alignment. + The results of a sequence alignment. Dan Berrios Dan Berrios aligned sequence data @@ -262,7 +262,7 @@ - The results of a data transformation of sequence data in which files containing aligned sequence data are merged together + 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 @@ -274,7 +274,7 @@ - The results of a sequence data feature count tabulation. + The results of a sequence data feature count tabulation. Dan Berrios Dan Berrios sequence library feature count data @@ -292,7 +292,7 @@ - The results of a DNA methylation profiling assay + The results of a DNA methylation profiling assay DNA methylation profiling data @@ -302,7 +302,7 @@ - The results of a differential expression analysis. + The results of a differential expression analysis. differential expression analysis data @@ -312,7 +312,7 @@ - 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 @@ -322,7 +322,7 @@ - Sequence data in which an identifier subsequence has been used to categorize each reads by source. + Sequence data in which an identifier subsequence has been used to categorize each reads by source. Dan Berrios Dan Berrios demultiplexed sequence data @@ -334,7 +334,7 @@ - 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. + 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 @@ -347,7 +347,7 @@ 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). + 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 @@ -362,7 +362,7 @@ 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). + 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 @@ -377,7 +377,7 @@ 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). + The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). Emma Griffiths input gene start query gene start site @@ -392,7 +392,7 @@ 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). + The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). Emma Griffiths input gene stop query gene stop site @@ -407,7 +407,7 @@ 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). + 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 @@ -422,7 +422,7 @@ 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). + 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 @@ -437,7 +437,7 @@ 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). + 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 @@ -452,7 +452,7 @@ 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). + The position of the last nucelotide in a reference sequence (sequence being used for comparison). Emma Griffiths reference gene stop subject gene stop site @@ -466,7 +466,7 @@ - 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. + 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 diff --git a/src/ontology/modules/specimen-assay-data.owl b/src/ontology/modules/specimen-assay-data.owl index 6599ce13..102001a4 100644 --- a/src/ontology/modules/specimen-assay-data.owl +++ b/src/ontology/modules/specimen-assay-data.owl @@ -208,7 +208,7 @@ - A data item that is the specified output of a blood assay. + A data item that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -231,7 +231,7 @@ - An organism detection datum that is the specified output of a blood microbiology assay. + An organism detection datum that is the specified output of a blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -254,7 +254,7 @@ - A data item that is the specified output of a feces assay. + A data item that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -277,7 +277,7 @@ - An organism detection datum that is the specified output of a feces microbiology assay. + An organism detection datum that is the specified output of a feces microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -300,7 +300,7 @@ - A data item that is the specified output of a urine assay. + A data item that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -323,7 +323,7 @@ - An organism detection datum that is the specified output of a urine microbiology assay. + An organism detection datum that is the specified output of a urine microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -346,7 +346,7 @@ - A data item that is the specified output of a induced sputum assay. + A data item that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -369,7 +369,7 @@ - An organism detection datum that is the specified output of an induced sputum microbiology assay. + An organism detection datum that is the specified output of an induced sputum microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -392,7 +392,7 @@ - A data item that is the specified output of a cerebrospinal fluid assay. + A data item that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -415,7 +415,7 @@ - An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. + An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -438,7 +438,7 @@ - An organism detection datum that is the specified output of an endotracheal aspirate assay. + An organism detection datum that is the specified output of an endotracheal aspirate assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -461,7 +461,7 @@ - An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. + An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -484,7 +484,7 @@ - An organism detection datum that is the specified output of a lung microbiology assay. + An organism detection datum that is the specified output of a lung microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -507,7 +507,7 @@ - An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. + An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -530,7 +530,7 @@ - An organism detection datum that is the specified output of a pleural fluid microbiology assay. + An organism detection datum that is the specified output of a pleural fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -553,7 +553,7 @@ - A data item that is the specified output of an umbilical cord blood assay. + A data item that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -576,7 +576,7 @@ - An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. + An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -599,7 +599,7 @@ - A blood microbiology datum that is about bacteria. + A blood microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -622,7 +622,7 @@ - A blood microbiology datum that is about a virus. + A blood microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -645,7 +645,7 @@ - A blood microbiology datum that is about eukaryota. + A blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -668,7 +668,7 @@ - A feces microbiology datum that is about bacteria. + A feces microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -691,7 +691,7 @@ - A feces microbiology datum that is about eukaryota. + A feces microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -714,7 +714,7 @@ - A feces microbiology datum that is about a virus. + A feces microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -737,7 +737,7 @@ - A urine microbiology datum that is about eukaryota. + A urine microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -760,7 +760,7 @@ - An induced sputum microbiology datum that is about bacteria. + An induced sputum microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -783,7 +783,7 @@ - An induced sputum microbiology datum that is about eukaryota. + An induced sputum microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -806,7 +806,7 @@ - An induced sputum microbiology datum that is about a virus. + An induced sputum microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -829,7 +829,7 @@ - An endotracheal tube aspirate microbiology datum that is about bacteria. + An endotracheal tube aspirate microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -852,7 +852,7 @@ - A lung microbiology datum that is about bacteria. + A lung microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -875,7 +875,7 @@ - A lung microbiology datum that is about eukaryota. + A lung microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -898,7 +898,7 @@ - A lung microbiology datum that is about a virus. + A lung microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -921,7 +921,7 @@ - A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria. + A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -944,7 +944,7 @@ - A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota. + A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -967,7 +967,7 @@ - A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus. + A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -990,7 +990,7 @@ - A pleural fluid microbiology datum that is about bacteria. + A pleural fluid microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -1013,7 +1013,7 @@ - A pleural fluid microbiology datum that is about eukaryota. + A pleural fluid microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -1036,7 +1036,7 @@ - A pleural fluid microbiology datum that is about a virus. + A pleural fluid microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -1059,7 +1059,7 @@ - An umbilical cord blood microbiology datum that is about eukaryota. + An umbilical cord blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -1112,7 +1112,7 @@ - A data item that is the specified output of a milk assay. + A data item that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 @@ -1141,7 +1141,7 @@ - An organism detection datum that is the specified output of a placental blood microbiology assay. + An organism detection datum that is the specified output of a placental blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 @@ -1164,7 +1164,7 @@ - A placental blood microbiology datum that is about eukaryota. + A placental blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 @@ -1187,7 +1187,7 @@ - A data item that is the specified output of an antigen specific antibodies assay. + A data item that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -1210,7 +1210,7 @@ - An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. + An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -1233,7 +1233,7 @@ - An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. + An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -1262,7 +1262,7 @@ - An organism detection datum that is the specified output of a skin of body microbiology assay. + An organism detection datum that is the specified output of a skin of body microbiology assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 @@ -1291,7 +1291,7 @@ - An organism detection datum that is the specified output of a bone marrow microbiology assay. + An organism detection datum that is the specified output of a bone marrow microbiology assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 @@ -1320,7 +1320,7 @@ - An organism detection datum that is the specified output of a nasal aspirate microbiology assay. + An organism detection datum that is the specified output of a nasal aspirate microbiology assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1680 diff --git a/src/ontology/modules/study-designs.owl b/src/ontology/modules/study-designs.owl index d343f396..d5a544de 100644 --- a/src/ontology/modules/study-designs.owl +++ b/src/ontology/modules/study-designs.owl @@ -257,7 +257,7 @@ 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. + 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 @@ -366,7 +366,7 @@ compound treatment design - an intervention design in which the treatment is the administration of a compound + 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 @@ -425,7 +425,7 @@ growth condition intervention design - A study design in which the independent variable is the environmental condition in which the specimen is growing + 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 @@ -457,7 +457,7 @@ 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 + 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 @@ -471,7 +471,7 @@ 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 + 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 @@ -517,7 +517,7 @@ operator variation design - A study design that assesses the operator performance and relation to data consistency and quality. + 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 @@ -537,7 +537,7 @@ comparative genome hybridization by array design - A study design that detects genomic copy number variations using microarray technology. + 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 @@ -550,7 +550,7 @@ - A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. + 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 @@ -564,7 +564,7 @@ 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. + 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 @@ -584,7 +584,7 @@ innate behavior design - A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. + 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 @@ -620,7 +620,7 @@ cell component comparison design - A study design that compares samples from different cell components. + 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 @@ -634,7 +634,7 @@ 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. + 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 @@ -670,7 +670,7 @@ normalization testing design - A study design that tests different normalization procedures. + A study design that tests different normalization procedures. Person: Chris Stoeckert, Jie Zheng MO_729 normalization_testing_design normalization testing design @@ -690,7 +690,7 @@ 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. + 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 @@ -715,7 +715,7 @@ - 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 + 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 @@ -751,7 +751,7 @@ array platform variation design - A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. + 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 @@ -777,7 +777,7 @@ 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. + 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 @@ -797,7 +797,7 @@ translational bias design - A study design that characterizes the association of transcripts and translation machinery. + 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 @@ -817,7 +817,7 @@ 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. + 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 @@ -831,7 +831,7 @@ 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. + 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 @@ -851,7 +851,7 @@ 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. + 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 @@ -871,7 +871,7 @@ transcription profiling by array design - A study design that identifies forms and abundance of transcripts in the genome using microarray technology. + 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 @@ -907,7 +907,7 @@ 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. + 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 @@ -937,7 +937,7 @@ RNA stability design - A study design that examines the stability and/or decay of RNA transcripts. + 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 @@ -973,7 +973,7 @@ species comparison design - A study design that assays differences between distinct species. + A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design @@ -993,7 +993,7 @@ 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). + 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 @@ -1013,7 +1013,7 @@ microRNA profiling by array design - A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. + 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 @@ -1053,7 +1053,7 @@ organism development design - A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. + 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 @@ -1073,7 +1073,7 @@ family history design - A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. + 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 @@ -1093,7 +1093,7 @@ quality control testing design - A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. + 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 @@ -1123,7 +1123,7 @@ clinical history design - A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. + 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 @@ -1159,7 +1159,7 @@ post-transcriptional modification design - A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. + 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 @@ -1190,7 +1190,7 @@ 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. + 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 @@ -1210,7 +1210,7 @@ injury design - A study design in which the response of an organism(s) to injury or damage is studied. + 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 @@ -1258,7 +1258,7 @@ organism status comparison design - A study design that compares samples from live and dead organisms. + 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 @@ -1272,7 +1272,7 @@ 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. + 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 @@ -1318,7 +1318,7 @@ 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. + 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 @@ -1344,7 +1344,7 @@ protocol optimization design - A study design where different protocols or protocol parameters are compared aims to find an optimized protocol + 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 @@ -1380,7 +1380,7 @@ 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. + 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 @@ -1407,7 +1407,7 @@ 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. + 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 @@ -1437,7 +1437,7 @@ 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. + 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 @@ -1457,7 +1457,7 @@ 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. + 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 @@ -1493,7 +1493,7 @@ cell type comparison design - A study design that compares cells of different type, for example different cell lines. + 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 @@ -1507,7 +1507,7 @@ 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. + 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 @@ -1576,7 +1576,7 @@ dose response design - A study design that examines the relationship between the size of the administered dose and the extent of the response. + 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 @@ -1612,7 +1612,7 @@ organism part comparison design - A study design that compares tissues, regions, organs within or between organisms + 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 @@ -1632,7 +1632,7 @@ protein binding site identification design - A study design that investigates protein binding sites on nucleic acids. + 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 @@ -1668,7 +1668,7 @@ sex comparison design - A study design that assays differences associated with an organism's sex, gender or mating type. + 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 @@ -1688,7 +1688,7 @@ 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. + 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 @@ -1718,7 +1718,7 @@ cell differentiation design - A study design that assays events associated with cell development or differentiation. + 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 @@ -1732,7 +1732,7 @@ transcription profiling design - A study design that identifies forms and abundance of transcripts in the genome. + 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 @@ -1752,7 +1752,7 @@ operon identification design - A study design that identifies locations and members of operons in a genome. + 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 @@ -1772,7 +1772,7 @@ 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. + 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 @@ -1786,7 +1786,7 @@ all pairs design - A study design in which all specimens are compared to every other specimen. + 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 @@ -1805,7 +1805,7 @@ - A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. + 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 @@ -1826,7 +1826,7 @@ genotyping design - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. + 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 @@ -1862,7 +1862,7 @@ individual genetic characteristics comparison design - A study design where genotype, haplotype, or other individual genetic characteristics are compared. + 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 @@ -1882,7 +1882,7 @@ 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. + 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 @@ -1925,7 +1925,7 @@ 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. + 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 @@ -1961,7 +1961,7 @@ strain comparison design - A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. + 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 @@ -2000,7 +2000,7 @@ - A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. + 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 @@ -2016,7 +2016,7 @@ 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. + 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 @@ -2045,7 +2045,7 @@ decision analysis study design - a study design that has a decision analysis objective specification as part + a study design that has a decision analysis objective specification as part PERSON: Bill Hogan PERSON: Bill Hogan decision analysis study design @@ -2057,7 +2057,7 @@ - A study design in which proteins in a sample are detected, quantified or otherwise analysed. + A study design in which proteins in a sample are detected, quantified or otherwise analysed. Dan Berrios OBI:0001441 proteomic profiling design @@ -2075,7 +2075,7 @@ - A study design that investigates the features of interaction between molecules. + A study design that investigates the features of interaction between molecules. Rebecca Jackson person:RCT molecular interaction identification design @@ -2087,7 +2087,7 @@ - A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. + 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 @@ -2115,7 +2115,7 @@ - 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. + 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 @@ -2127,7 +2127,7 @@ - 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. + 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 @@ -2155,7 +2155,7 @@ - A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. + 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 @@ -2168,7 +2168,7 @@ - A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. + 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 @@ -2180,7 +2180,7 @@ - A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. + 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 @@ -2193,7 +2193,7 @@ 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. + 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 @@ -2206,7 +2206,7 @@ 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. + 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 @@ -2218,7 +2218,7 @@ - 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. + 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 @@ -2233,7 +2233,7 @@ 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. + 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 @@ -2246,7 +2246,7 @@ 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. + 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 https://github.com/obi-ontology/obi/issues/1090 @@ -2259,7 +2259,7 @@ - A study design that is executed primarily on a computer. + 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 @@ -2275,7 +2275,7 @@ ring trial design https://eco-fab.org/about-ecofab-initiative/ - A study design with the objective of establishing the reproducibility of an experimental approach by performing experiments in different laboratories under the same conditions and comparing the experimental outcomes. + A study design with the objective of establishing the reproducibility of an experimental approach by performing experiments in different laboratories under the same conditions and comparing the experimental outcomes. Bjoern Peters Sebastian Duesing https://github.com/obi-ontology/obi/issues/1768 @@ -2304,7 +2304,7 @@ 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 + 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 @@ -2320,7 +2320,7 @@ 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. + 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 @@ -2341,7 +2341,7 @@ 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] + 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 @@ -2357,7 +2357,7 @@ 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 + 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 @@ -2372,7 +2372,7 @@ 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 + 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 @@ -2386,7 +2386,7 @@ 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). + 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 @@ -2401,7 +2401,7 @@ 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. + 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 @@ -2416,7 +2416,7 @@ 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 + 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 @@ -2432,7 +2432,7 @@ 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. + 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 @@ -2447,7 +2447,7 @@ 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' + 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 @@ -2462,7 +2462,7 @@ loop design PMID: 12933549 - A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular 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 @@ -2477,7 +2477,7 @@ reference design PMID: 12933549 - A reference experiment design type is where all samples are compared to a common reference. + 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 @@ -2492,7 +2492,7 @@ 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. + 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 @@ -2507,7 +2507,7 @@ 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 + 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 @@ -2522,7 +2522,7 @@ hyper graeco latin square design - PRS to do + 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 @@ -2537,7 +2537,7 @@ 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. + 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 @@ -2552,7 +2552,7 @@ 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 + 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 @@ -2566,7 +2566,7 @@ 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 + 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 @@ -2581,7 +2581,7 @@ 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 + 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 @@ -2595,7 +2595,7 @@ 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. + 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 @@ -2610,7 +2610,7 @@ 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. + 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 @@ -2625,7 +2625,7 @@ 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. + Groups of assays that are related as part of a time series. Philippe Rocca-Serra on behalf of MO MO_887 time series design diff --git a/src/ontology/modules/value-specifications.owl b/src/ontology/modules/value-specifications.owl index eb0ea9a3..57e71d3c 100644 --- a/src/ontology/modules/value-specifications.owl +++ b/src/ontology/modules/value-specifications.owl @@ -104,7 +104,7 @@ cannot be assessed, not applicable, unknown - An information content entity that provides an explanation why a data item is not provided. + An information content entity that provides an explanation why a data item is not provided. Chris Stoeckert, Helena Ellis OBI NCI BBRB @@ -117,7 +117,7 @@ - A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. + 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 @@ -131,7 +131,7 @@ - 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. + 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 @@ -145,7 +145,7 @@ AJCC 7th edition GX: cannot be assessed. - A cannot be assessed determination for histologic tumor grade. + A cannot be assessed determination for histologic tumor grade. Chris Stoeckert, Helena Ellis OBI NCI BBRB @@ -159,7 +159,7 @@ AJCC 7th edition pTX: cannot be assessed. - A cannot be assessed determination for pathologic primary tumor staging. + A cannot be assessed determination for pathologic primary tumor staging. Chris Stoeckert, Helena Ellis OBI NCI BBRB @@ -173,7 +173,7 @@ AJCC 7th edition pNX: cannot be assessed. - A cannot be assessed determination of pathologic staging of lymph nodes. + A cannot be assessed determination of pathologic staging of lymph nodes. Chris Stoeckert, Helena Ellis OBI NCI BBRB @@ -188,7 +188,7 @@ 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. + 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 @@ -201,7 +201,7 @@ - A categorical value specification that is a histologic grade assigned to a tumor slide specimen 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 @@ -215,7 +215,7 @@ - A categorical value specification that is a histologic grade assigned to a 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 @@ -228,7 +228,7 @@ - A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + 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 @@ -241,7 +241,7 @@ - A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + 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 @@ -254,7 +254,7 @@ - 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. + 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 @@ -268,7 +268,7 @@ - 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. + 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 @@ -282,7 +282,7 @@ - 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. + 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 @@ -296,7 +296,7 @@ - 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. + 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 @@ -310,7 +310,7 @@ - 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. + 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 @@ -324,7 +324,7 @@ - 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. + 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 @@ -338,7 +338,7 @@ - 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. + 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 @@ -352,7 +352,7 @@ - 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. + 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 @@ -366,7 +366,7 @@ - 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. + 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 @@ -380,7 +380,7 @@ - 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. + 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 @@ -394,7 +394,7 @@ - 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. + 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 @@ -408,7 +408,7 @@ - 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. + 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 @@ -422,7 +422,7 @@ - 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. + 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 @@ -436,7 +436,7 @@ - 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. + 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 @@ -450,7 +450,7 @@ - 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. + 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 @@ -464,7 +464,7 @@ - A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + 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 @@ -478,7 +478,7 @@ - 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. + 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 @@ -492,7 +492,7 @@ - A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + 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 @@ -506,7 +506,7 @@ - A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material + 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 @@ -520,7 +520,7 @@ - A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment + 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 @@ -535,7 +535,7 @@ hypertension grade - A categorical value specification that indicates the severity of hypertension. + A categorical value specification that indicates the severity of hypertension. Bjoern Peters Randi Vita Sebastian Duesing @@ -559,7 +559,7 @@ - A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + 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 @@ -573,7 +573,7 @@ - A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + 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 @@ -587,7 +587,7 @@ - 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. + 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 @@ -601,7 +601,7 @@ - A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + 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 @@ -615,7 +615,7 @@ - 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. + 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 @@ -629,7 +629,7 @@ - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + 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 @@ -643,7 +643,7 @@ - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + 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 @@ -657,7 +657,7 @@ - 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. + 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 @@ -671,7 +671,7 @@ - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + 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 @@ -685,7 +685,7 @@ - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + 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 @@ -699,7 +699,7 @@ - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + 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 @@ -713,7 +713,7 @@ - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + 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 @@ -727,7 +727,7 @@ - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + 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 @@ -741,7 +741,7 @@ - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + 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 @@ -755,7 +755,7 @@ - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + 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 @@ -768,7 +768,7 @@ - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + 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 @@ -781,7 +781,7 @@ - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + 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 @@ -794,7 +794,7 @@ - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + 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 @@ -807,7 +807,7 @@ - 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. + 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 @@ -820,7 +820,7 @@ - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + 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 @@ -833,7 +833,7 @@ - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + 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 @@ -846,7 +846,7 @@ - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + 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 @@ -859,7 +859,7 @@ - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + 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 @@ -872,7 +872,7 @@ - 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). + 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 @@ -885,7 +885,7 @@ - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + 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 @@ -898,7 +898,7 @@ - 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. + 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 @@ -911,7 +911,7 @@ - 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. + 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 @@ -924,7 +924,7 @@ - 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. + 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 @@ -937,7 +937,7 @@ - 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. + 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 @@ -950,7 +950,7 @@ - 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. + 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 @@ -963,7 +963,7 @@ - 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. + 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 @@ -976,7 +976,7 @@ - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + 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 @@ -989,7 +989,7 @@ - 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. + 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 @@ -1002,7 +1002,7 @@ - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + 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 @@ -1015,7 +1015,7 @@ - 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. + 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 @@ -1028,7 +1028,7 @@ - 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. + 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 @@ -1041,7 +1041,7 @@ - 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. + 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 @@ -1054,7 +1054,7 @@ - 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. + 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 @@ -1067,7 +1067,7 @@ - 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. + 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 @@ -1080,7 +1080,7 @@ - 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. + 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 @@ -1093,7 +1093,7 @@ - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + 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 @@ -1106,7 +1106,7 @@ - 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. + 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 @@ -1119,7 +1119,7 @@ - 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). + 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 @@ -1132,7 +1132,7 @@ - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + 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 @@ -1145,7 +1145,7 @@ - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + 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 @@ -1158,7 +1158,7 @@ - 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. + 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 @@ -1171,7 +1171,7 @@ - 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. + 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 @@ -1184,7 +1184,7 @@ - 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. + 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 @@ -1197,7 +1197,7 @@ - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + 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 @@ -1210,7 +1210,7 @@ - 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. + 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 @@ -1223,7 +1223,7 @@ - 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. + 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 @@ -1236,7 +1236,7 @@ - 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. + 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 @@ -1249,7 +1249,7 @@ - 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. + 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 @@ -1262,7 +1262,7 @@ - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + 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 @@ -1275,7 +1275,7 @@ - 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. + 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 @@ -1288,7 +1288,7 @@ - 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. + 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 @@ -1301,7 +1301,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + 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 @@ -1314,7 +1314,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + 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 @@ -1327,7 +1327,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + 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 @@ -1340,7 +1340,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + 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 @@ -1353,7 +1353,7 @@ - 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. + 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 @@ -1366,7 +1366,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + 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 @@ -1379,7 +1379,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + 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 @@ -1392,7 +1392,7 @@ - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + 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 @@ -1405,7 +1405,7 @@ - A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + 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 @@ -1418,7 +1418,7 @@ - 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. + 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 @@ -1431,7 +1431,7 @@ - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + 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 @@ -1444,7 +1444,7 @@ - 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). + 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 @@ -1457,7 +1457,7 @@ - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + 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 @@ -1470,7 +1470,7 @@ - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + 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 @@ -1483,7 +1483,7 @@ - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + 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 @@ -1496,7 +1496,7 @@ - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + 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 @@ -1509,7 +1509,7 @@ - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + 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 @@ -1522,7 +1522,7 @@ - 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. + 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 @@ -1535,7 +1535,7 @@ - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + 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 @@ -1548,7 +1548,7 @@ - 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. + 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 @@ -1561,7 +1561,7 @@ - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + 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 @@ -1574,7 +1574,7 @@ - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + 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 @@ -1587,7 +1587,7 @@ - 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. + 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 @@ -1600,7 +1600,7 @@ - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + 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 @@ -1613,7 +1613,7 @@ - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + 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 @@ -1626,7 +1626,7 @@ - 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. + 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 @@ -1639,7 +1639,7 @@ - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + 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 @@ -1652,7 +1652,7 @@ - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + 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 @@ -1665,7 +1665,7 @@ - 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. + 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 @@ -1678,7 +1678,7 @@ - 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. + 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 @@ -1691,7 +1691,7 @@ - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + 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 @@ -1704,7 +1704,7 @@ - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + 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 @@ -1717,7 +1717,7 @@ - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + 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 @@ -1730,7 +1730,7 @@ - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + 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 @@ -1743,7 +1743,7 @@ - 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. + 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 @@ -1756,7 +1756,7 @@ - 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. + 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 @@ -1769,7 +1769,7 @@ - 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. + 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 @@ -1783,7 +1783,7 @@ - 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. + 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 @@ -1797,7 +1797,7 @@ - A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + 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 @@ -1811,7 +1811,7 @@ - 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. + 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 @@ -1825,7 +1825,7 @@ - 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. + 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 @@ -1839,7 +1839,7 @@ - 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. + 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 @@ -1853,7 +1853,7 @@ - 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. + 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 @@ -1867,7 +1867,7 @@ - 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. + 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 @@ -1881,7 +1881,7 @@ - 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. + 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 @@ -1895,7 +1895,7 @@ - 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. + 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 @@ -1909,7 +1909,7 @@ - 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. + 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 @@ -1923,7 +1923,7 @@ - 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. + 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 @@ -1937,7 +1937,7 @@ - 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. + 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 @@ -1951,7 +1951,7 @@ - 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. + 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 @@ -1965,7 +1965,7 @@ - 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 + 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 @@ -1979,7 +1979,7 @@ - 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. + 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 @@ -1993,7 +1993,7 @@ - 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. + 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 @@ -2007,7 +2007,7 @@ - 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. + 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 @@ -2021,7 +2021,7 @@ - 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. + 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 @@ -2035,7 +2035,7 @@ - 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. + 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 @@ -2049,7 +2049,7 @@ - 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. + 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 @@ -2063,7 +2063,7 @@ - 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. + 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 @@ -2077,7 +2077,7 @@ - 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. + 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 @@ -2091,7 +2091,7 @@ - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + 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 @@ -2105,7 +2105,7 @@ - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + 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 @@ -2119,7 +2119,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + 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/ @@ -2133,7 +2133,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + 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/ @@ -2147,7 +2147,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + 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/ @@ -2161,7 +2161,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + 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/ @@ -2175,7 +2175,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + 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/ @@ -2189,7 +2189,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + 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/ @@ -2203,7 +2203,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + 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/ @@ -2217,7 +2217,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + 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/ @@ -2231,7 +2231,7 @@ - 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). + 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/ @@ -2245,7 +2245,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + 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/ @@ -2259,7 +2259,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + 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/ @@ -2273,7 +2273,7 @@ - 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). + 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/ @@ -2287,7 +2287,7 @@ - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + 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/ @@ -2301,7 +2301,7 @@ - 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). + 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/ @@ -2315,7 +2315,7 @@ - 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. + 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 @@ -2328,7 +2328,7 @@ - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for 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 @@ -2341,7 +2341,7 @@ - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is 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 @@ -2354,7 +2354,7 @@ - An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -2367,7 +2367,7 @@ - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is 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 @@ -2380,7 +2380,7 @@ - A Karnofsky score vaue specification indicating that a patient is asymptomatic. + A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB @@ -2393,7 +2393,7 @@ - A Karnofsky score vaue specification indicating that a patient is 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 @@ -2406,7 +2406,7 @@ - A Karnofsky score vaue specification indicating that a patient is 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 @@ -2419,7 +2419,7 @@ - A Karnofsky score vaue specification indicating that a patient is 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 From 360cfe7fcd320393d83e73fd53ed25e4d2a1d128 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 11 Jul 2024 13:14:23 -0500 Subject: [PATCH 3/3] Remove extra space from obi-edit language tags --- src/ontology/obi-edit.owl | 1362 ++++++++++++++++++------------------- 1 file changed, 681 insertions(+), 681 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index e9c418e5..f0ece3b6 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -301,7 +301,7 @@ - An alternative term used by the ISA tools project (http://isa-tools.org). + An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran @@ -317,7 +317,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). + An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term @@ -330,7 +330,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An alternative term used by the IEDB. + An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term @@ -343,7 +343,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - An alternative term used by the Functional Genomics Data (FGED) Society. + An alternative term used by the Functional Genomics Data (FGED) Society. PERSON: Chris Stoeckert, Jie Zheng Penn Group FGED alternative term @@ -651,7 +651,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. - A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. + A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with @@ -664,7 +664,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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 @@ -698,7 +698,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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. + 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 @@ -730,7 +730,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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. + 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 @@ -747,7 +747,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 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 @@ -784,7 +784,7 @@ 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] + 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 @@ -837,7 +837,7 @@ 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 - Relation between an independent continuant and a function. + 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 @@ -874,7 +874,7 @@ 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 @@ -997,7 +997,7 @@ level of radioactivity is_proxy_for level of toxicity has_role - A relation between a continuant C and a role R. The reciprocal relation of role_of. + 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 @@ -1030,7 +1030,7 @@ 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. + 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 @@ -1044,7 +1044,7 @@ level of radioactivity is_proxy_for level of toxicity 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. + 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 @@ -1060,7 +1060,7 @@ level of radioactivity is_proxy_for level of toxicity 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 @@ -1074,7 +1074,7 @@ level of radioactivity is_proxy_for level of toxicity obsoleted_is_specified_information_intput_of - Is the inverse relation of has_specfied_input_information + Is the inverse relation of has_specfied_input_information is replaced by is_specified_intput_of obsoleted_is_specified_information_intput_of @@ -1088,7 +1088,7 @@ level of radioactivity is_proxy_for level of toxicity 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. + 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. PERSON: Alan Ruttenberg Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 @@ -1102,7 +1102,7 @@ level of radioactivity is_proxy_for level of toxicity 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 supplies @@ -1125,7 +1125,7 @@ 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. + 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 @@ -1142,7 +1142,7 @@ level of radioactivity is_proxy_for level of toxicity 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 @@ -1164,7 +1164,7 @@ 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. + 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 @@ -1184,7 +1184,7 @@ level of radioactivity is_proxy_for level of toxicity 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. + 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 @@ -1197,7 +1197,7 @@ level of radioactivity is_proxy_for level of toxicity has disposition to bind - A relationship between two material entitites that each have disposition to form a complex with the other. + 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 @@ -1217,7 +1217,7 @@ level of radioactivity is_proxy_for level of toxicity - Relating an organization to a legal person or organization. + 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 @@ -1231,7 +1231,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a value specification and an entity which the specification is about. + A relation between a value specification and an entity which the specification is about. specifies value of @@ -1244,7 +1244,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between an information content entity and a value specification that specifies its value. + A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification @@ -1275,7 +1275,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. + A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI OBI The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). @@ -1288,7 +1288,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. + A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1516 @@ -1305,7 +1305,7 @@ 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 - is a relationship between a process and a preceding occurrent that directly caused the later one to occur + 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 @@ -1331,7 +1331,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ bound_to - A relationship between two material entities that form a complex based on a selective, non-covalent interaction. + 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 @@ -1481,7 +1481,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a value specification and a number that quantifies it. + A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI @@ -1494,7 +1494,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A relation between a value specification and a literal. + A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value @@ -3160,7 +3160,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ 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 OBI, CDISC @@ -3371,7 +3371,7 @@ 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 - A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization + 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 @@ -3441,7 +3441,7 @@ 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 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. + 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 @@ -3630,7 +3630,7 @@ objectives is a planned process. 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 role @@ -3917,7 +3917,7 @@ editor = PRS 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. + 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 @@ -3988,7 +3988,7 @@ In regard to the statement that reagents are 'distinct' from the speci detector reagent role - a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. + 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 @@ -4003,7 +4003,7 @@ In regard to the statement that reagents are 'distinct' from the speci 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 + 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 @@ -4103,7 +4103,7 @@ In regard to the statement that reagents are 'distinct' from the speci 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 @@ -4193,7 +4193,7 @@ editor = PRS 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 @@ -4331,7 +4331,7 @@ 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 @@ -4371,7 +4371,7 @@ specimen can later be subject. 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 role @@ -4462,7 +4462,7 @@ specimen can later be subject. 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 - the role of a organization that is realized by members reviewing study designs for their agreement with regulations + 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 @@ -4493,7 +4493,7 @@ specimen can later be subject. 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 role @@ -4508,7 +4508,7 @@ specimen can later be subject. 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 role @@ -4584,7 +4584,7 @@ addition of has_role restriction 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 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. @@ -4708,7 +4708,7 @@ http://code.google.com/p/popcomm-ontology/ 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: Jennifer Fostel @@ -4739,7 +4739,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 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 OBI @@ -4898,7 +4898,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 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 role @@ -4914,7 +4914,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 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 @@ -4988,7 +4988,7 @@ An individual or juridicial or other body authorized under applicable law to con vital dye role typtan blue has a vital dye - A dye role that is realized when used to detect live cells in an experiment + 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 @@ -5237,7 +5237,7 @@ for now. 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 OBI @@ -5253,7 +5253,7 @@ for now. 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 role @@ -5267,7 +5267,7 @@ 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 @@ -5895,7 +5895,7 @@ Proposal is to obsolete. 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. + 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 @@ -5941,7 +5941,7 @@ 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. + 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 @@ -6279,7 +6279,7 @@ Proposal is to obsolete. 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. + 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 @@ -6325,7 +6325,7 @@ 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 - The extraction of RNA from an input material that specifically isolates viral RNA + The extraction of RNA from an input material that specifically isolates viral RNA Person:Bjoern Peters viral RNA extraction @@ -6351,7 +6351,7 @@ Proposal is to obsolete. 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 @@ -6373,7 +6373,7 @@ Proposal is to obsolete. recombinant plasmid - a plasmid in which extraneous DNA has been inserted. + a plasmid in which extraneous DNA has been inserted. PERSON: Bjoern Peters PERSON: Kevin Clancy PERSON: Melanie Courtot @@ -6759,7 +6759,7 @@ 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 - A process in which an input substance is injected into a organ section. + A process in which an input substance is injected into a organ section. Person:Bjoern Peters injection into organ section @@ -6878,7 +6878,7 @@ 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. - A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. + A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. 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 @@ -7086,7 +7086,7 @@ 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. - a planned process that carries out 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. @@ -7120,7 +7120,7 @@ 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. - a process in which a population of cells with certain characteristics is isolated from a larger 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 @@ -7145,7 +7145,7 @@ that has_part some material entity is a material entity. If we add as equivalent 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. + 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 @@ -7176,7 +7176,7 @@ 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. - a process in which cells with a single nucleus are isolated from a blood sample + 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 @@ -7222,7 +7222,7 @@ that has_part some material entity is a material entity. If we add as equivalent 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. + 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 @@ -7258,7 +7258,7 @@ 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 is a role which inheres in a person or organization and which is realized by a manufacturing process. + 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 @@ -7309,7 +7309,7 @@ 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. - is an objective to transform a material entity into spatially separated components. + is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective @@ -7407,7 +7407,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 urine specimen - a portion of urine collected from an organism + 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? @@ -7441,7 +7441,7 @@ 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. - is a material processing with the objective to combine two or more material entities as input into a single material entity as output. + 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 @@ -7478,7 +7478,7 @@ 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 - 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 @@ -7511,7 +7511,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 blood specimen blood drawn from a human for glucose assay - a material entity derived from a portion of blood collected from an organism + a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen @@ -7548,7 +7548,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 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. + 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 @@ -7587,7 +7587,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 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. + 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. @@ -7746,7 +7746,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ sample from organism - a material obtained from an organism in order to be a representative of the whole + 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 @@ -7801,7 +7801,7 @@ 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 @@ -7839,7 +7839,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective @@ -7896,7 +7896,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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 + 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 @@ -7910,7 +7910,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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). + 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 @@ -7923,7 +7923,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective @@ -7962,7 +7962,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -7976,7 +7976,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ material combination objective - is an objective to obtain an output material that contains several input materials. + is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective @@ -7991,7 +7991,7 @@ 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 is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation + 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 @@ -8005,7 +8005,7 @@ 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. - A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. + 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 @@ -8032,7 +8032,7 @@ 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. - is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity + 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 @@ -8046,7 +8046,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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 + 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 @@ -8077,7 +8077,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ animal feeding giving crickets to a snake. - animal feeding is a process in which animals are provided with food + 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 @@ -8098,7 +8098,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -8135,7 +8135,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -8151,7 +8151,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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. + 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 @@ -8211,7 +8211,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ laboratory animal care - a process that realizes an animal care protocol that specifies how animals are kept and maintained + a process that realizes an animal care protocol that specifies how animals are kept and maintained laboratory animal care @@ -8229,7 +8229,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ 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 + 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 @@ -8279,7 +8279,7 @@ 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. - 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. + 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 @@ -8351,7 +8351,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ pathogen challenge - The administration of a live pathogenic organism to a host. + The administration of a live pathogenic organism to a host. pathogen challenge @@ -8363,7 +8363,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ GenePattern software - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + 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/ @@ -8379,7 +8379,7 @@ 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. - 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. + 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 @@ -8396,7 +8396,7 @@ 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. - An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes + 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 @@ -8423,7 +8423,7 @@ 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 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 + 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 @@ -8445,7 +8445,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ vaccine preparation The production of B. pertussis vaccine. - A planned process with the objective to create a vaccine. + A planned process with the objective to create a vaccine. OBI vaccine production @@ -8465,7 +8465,7 @@ 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 - The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. + 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 @@ -8484,7 +8484,7 @@ 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. - is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs + 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 @@ -8507,7 +8507,7 @@ 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 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 + 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 @@ -8524,7 +8524,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -8620,7 +8620,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8644,7 +8644,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8668,7 +8668,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8687,7 +8687,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -8713,7 +8713,7 @@ the role 'adjuvant role' inheres in some 'material entity' a NTP-2000 - a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents + a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents Jennifer Fostel, Bjoern Peters NTP-2000 @@ -8726,7 +8726,7 @@ the role 'adjuvant role' inheres in some 'material entity' a single fragment library - is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs + 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 @@ -8756,7 +8756,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8806,7 +8806,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8831,7 +8831,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -8846,7 +8846,7 @@ 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. - A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. + 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 @@ -8861,7 +8861,7 @@ 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. - 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. + 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 @@ -8899,7 +8899,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -8926,7 +8926,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 @@ -8952,7 +8952,7 @@ 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. - A material entity that has the material sample role + A material entity that has the material sample role OBI: workshop sample population @@ -9090,7 +9090,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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 + 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 @@ -9102,7 +9102,7 @@ the role 'adjuvant role' inheres in some 'material entity' a 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. + 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 @@ -9117,7 +9117,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9131,7 +9131,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9152,7 +9152,7 @@ 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 - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + 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 @@ -9187,7 +9187,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9203,7 +9203,7 @@ 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. - 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 + 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 @@ -9219,7 +9219,7 @@ http://en.wikipedia.org/wiki/Survival_rate capsule shell - a small rounded gelatinous container + 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 @@ -9235,7 +9235,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9262,7 +9262,7 @@ 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 - A process in which bonds are created that link one polymer to another + 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 @@ -9277,7 +9277,7 @@ 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 - A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. + 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 @@ -9313,7 +9313,7 @@ http://en.wikipedia.org/wiki/Survival_rate denaturing Denaturing DNA in alcohol - Is a process in which the tertiary or secondary structure of a polymer is disrupted + Is a process in which the tertiary or secondary structure of a polymer is disrupted http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denaturing @@ -9356,7 +9356,7 @@ http://en.wikipedia.org/wiki/Survival_rate informing investigator of subject study arm Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound. - A planned process with the objective to make the investigator aware of which study arm a patient is participating in. + A planned process with the objective to make the investigator aware of which study arm a patient is participating in. 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 @@ -9371,7 +9371,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance objective - An objective specification maintains some or all of the qualities of a material over time. + An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective @@ -9402,7 +9402,7 @@ http://en.wikipedia.org/wiki/Survival_rate presentation of stimulus The presentation of a flashing light to a monkey during reward training - A planned process with the objective to expose an organism to a stimulus. + A planned process with the objective to expose an organism to a stimulus. Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom @@ -9429,7 +9429,7 @@ http://en.wikipedia.org/wiki/Survival_rate amplified DNA Amplied DNA created by PCR - DNA that has been produced in an enzymatic amplification process + DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA @@ -9460,7 +9460,7 @@ http://en.wikipedia.org/wiki/Survival_rate informed consent process - A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. + A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in 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 @@ -9487,7 +9487,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9502,7 +9502,7 @@ 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 - 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 + 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 @@ -9517,7 +9517,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9531,7 +9531,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9546,7 +9546,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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). + 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 @@ -9573,7 +9573,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9611,7 +9611,7 @@ http://en.wikipedia.org/wiki/Survival_rate anticoagulant tube storage of blood specimen - Storage of a blood specimen in a tube with anticoagulant + 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 @@ -9631,7 +9631,7 @@ http://en.wikipedia.org/wiki/Survival_rate filled capsule - A pill in the form of a small rounded gelatinous container with medicine inside. + 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 @@ -9660,7 +9660,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9676,7 +9676,7 @@ 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 is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material + 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 @@ -9690,7 +9690,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9710,7 +9710,7 @@ http://en.wikipedia.org/wiki/Survival_rate treatment portion of study execution - A planned process, part of a study design execution, during which the treatment of subjects is ongoing + 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 @@ -9725,7 +9725,7 @@ http://en.wikipedia.org/wiki/Survival_rate pill - A dose of medicine or placebo in the form of a small pellet. + 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 @@ -9741,7 +9741,7 @@ http://en.wikipedia.org/wiki/Survival_rate research organization The SALK institute is a research organization. - An organization formed with a goal to have its members conduct investigations + An organization formed with a goal to have its members conduct investigations Person:Bjoern Peters research organization @@ -9754,7 +9754,7 @@ http://en.wikipedia.org/wiki/Survival_rate DNA residue methylation - a quality of a DNA residue that has a methyl group attached to it + a quality of a DNA residue that has a methyl group attached to it DNA residue methylation @@ -9767,7 +9767,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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. + 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 @@ -9797,7 +9797,7 @@ http://en.wikipedia.org/wiki/Survival_rate manufacturer - A person or organization that has a manufacturer role. + A person or organization that has a manufacturer role. manufacturer @@ -9815,7 +9815,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance - A planned process with the objective to maintain some or all of the characteristics of an input material over time. + A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance @@ -9840,7 +9840,7 @@ http://en.wikipedia.org/wiki/Survival_rate 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 + 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 @@ -9869,7 +9869,7 @@ placeholder unblinding process - A planned process that is 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. + A planned process that is 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 @@ -9889,7 +9889,7 @@ placeholder subject agrees they understand informed consent document - A planned process in which a subject receives an informed consent document and agrees that they have understood it. + A planned 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 @@ -9924,7 +9924,7 @@ placeholder informing subject of study arm Informing participants whether they are receiving a placebo or a treatment with an investigational compound. - A planned process with the objective to make the subject aware of which study arm they are participating in. + A planned process with the objective to make the subject aware of which study arm they are participating in. 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 @@ -9950,7 +9950,7 @@ placeholder 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 + 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 @@ -9964,7 +9964,7 @@ placeholder 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 + 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 @@ -9978,7 +9978,7 @@ placeholder polyA RNA extraction - A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. + 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 @@ -9993,7 +9993,7 @@ placeholder organellar RNA extraction - A RNA extraction process in which the desired output material is RNA in the organelle(s). + A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10009,7 +10009,7 @@ 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. - An information content entity created to indicate that information about something is not available to the person recording it. + An 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 @@ -10024,7 +10024,7 @@ placeholder total RNA extraction - A RNA extraction process in which total cellular and organelle RNA are extracted. + A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10047,7 +10047,7 @@ placeholder 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 + 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 @@ -10067,7 +10067,7 @@ 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. - a record indicating that the biological sex of an organism is not known. + 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 @@ -10081,7 +10081,7 @@ placeholder cytoplasmic RNA extraction - A RNA extraction process in which the desired output material is RNA in the cytoplasm. + A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10096,7 +10096,7 @@ placeholder 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. + 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 @@ -10116,7 +10116,7 @@ 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) - 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. + 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 @@ -10138,7 +10138,7 @@ placeholder 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 + 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 @@ -10152,7 +10152,7 @@ placeholder 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. + 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 @@ -10173,7 +10173,7 @@ 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.) - 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. + 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 @@ -10216,7 +10216,7 @@ placeholder pre-mortem specimen material obtained through a liver biopsy from a human patient - a specimen that was taken from a live organism + a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen @@ -10237,7 +10237,7 @@ 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.) - A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. + 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 @@ -10265,7 +10265,7 @@ placeholder 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 'establishing immortal cell line through directed genetic modification' @@ -10284,7 +10284,7 @@ placeholder 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 + 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 @@ -10313,7 +10313,7 @@ Person: Chris Stoeckert RNA extract - an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. + 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 @@ -10328,7 +10328,7 @@ Person: Chris Stoeckert 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 @@ -10344,7 +10344,7 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La nuclear RNA extraction - A RNA extraction process in which the desired output material is RNA in the nucleus. + A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group @@ -10395,7 +10395,7 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La 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, + 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 @@ -10416,7 +10416,7 @@ 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. - A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. + 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 @@ -10432,7 +10432,7 @@ 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. - + 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 @@ -10453,7 +10453,7 @@ 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. - 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. + 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 @@ -10495,7 +10495,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. post mortem specimen the spleen taken from a dead mouse - a specimen that was taken from a dead organism + a specimen that was taken from a dead organism Bjoern Peters MO_416 postmortem post mortem specimen @@ -10509,7 +10509,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. sequence feature annotation - Information about a sequence region + Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term @@ -10530,7 +10530,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. induced hemagglutination - The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances + 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 @@ -10555,7 +10555,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t supplying Jackson Labs supplies mouse strains. - A planned process with the objective to provide material entities to be used in an investigation. + A planned process with the objective to provide 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. @@ -10600,7 +10600,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t 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. + 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 @@ -10623,7 +10623,7 @@ Added duirng Mar 1, 2010 dev call 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 @@ -10646,7 +10646,7 @@ stained with fecal material and is then placed in transport medium.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 @@ -10702,7 +10702,7 @@ aspiration. freezing storage a fozen pellet used for later assay - A storage process in temperature that maintenance the frozen status of the stored entities. + 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. @@ -10733,7 +10733,7 @@ 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 - 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 @@ -10762,7 +10762,7 @@ exudate and epithelial debris for microbiological or cellular examination. Dulbecco's modified Eagle medium - A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. + 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 @@ -10785,7 +10785,7 @@ exudate and epithelial debris for microbiological or cellular examination.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 + 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 @@ -10831,7 +10831,7 @@ exudate and epithelial debris for microbiological or cellular examination. 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. + 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 @@ -10881,7 +10881,7 @@ Added duirng Mar 1, 2010 dev call frozen specimen Frozen blood plasma - A specimen that has been frozen in order to store it. + A specimen that has been frozen in order to store it. Person:Alan Ruttenberg MO_610 frozen_sample frozen specimen @@ -10909,7 +10909,7 @@ Added duirng Mar 1, 2010 dev call labeled specimen - A specimen that has been modified in order to be able to detect it in future experiments + 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 @@ -10956,7 +10956,7 @@ Added duirng Mar 1, 2010 dev call lyophilization storage - a storage process with input material entity and output freeze dried material for long time storage + a storage process with input material entity and output freeze dried material for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng @@ -10973,7 +10973,7 @@ Added duirng Mar 1, 2010 dev call 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. + A material separation function is a function that decreases the resolution between two or more material entities. Helen Parkinson OBI material combination function @@ -11022,7 +11022,7 @@ Added duirng Mar 1, 2010 dev call study intervention - A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. + A planned process that is 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 @@ -11042,7 +11042,7 @@ Added duirng Mar 1, 2010 dev call categorical measurement datum - A measurement datum that is reported on a categorical scale. + A measurement datum that is reported on a categorical scale. Bjoern Peters nominal mesurement datum Bjoern Peters @@ -11064,7 +11064,7 @@ 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 - a process that achieves a training objective + a process that achieves a training objective training process @@ -11090,7 +11090,7 @@ Added duirng Mar 1, 2010 dev call 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 + a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role @@ -11134,7 +11134,7 @@ Added duirng Mar 1, 2010 dev call 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 + 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 @@ -11148,7 +11148,7 @@ Biochimie. 2010 Feb 18. sterilization function - a function to remove viable organisms from an input material + a function to remove viable organisms from an input material sterilization function @@ -11180,7 +11180,7 @@ 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. - 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 + 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 @@ -11194,7 +11194,7 @@ 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 - is realized in a planned process where the bearer participates + 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 @@ -11240,7 +11240,7 @@ Biochimie. 2010 Feb 18. paraffin specimen liver tissue embedded in paraffin - a specimen that is output of a paraffin storage process in which specimen is 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 @@ -11264,7 +11264,7 @@ Biochimie. 2010 Feb 18. 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. + 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. @@ -11280,7 +11280,7 @@ 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. - A function that is realized when a reagent is automatically added to some research material. + 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? @@ -11296,7 +11296,7 @@ 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. - A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. + 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 @@ -11311,7 +11311,7 @@ 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 - An objective specification which is fulfilled by the provision of some training. + An objective specification which is fulfilled by the provision of some training. Helen Parkinson OBI training objective @@ -11326,7 +11326,7 @@ 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. - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + 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 @@ -11372,7 +11372,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.lyophilized specimen freezing dried DNA - a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. + 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 @@ -11412,7 +11412,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells.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. + 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: @@ -11439,7 +11439,7 @@ 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 - a directive information entity that describes the dose that will be administered to a target + a directive information entity that describes the dose that will be administered to a target dose specification @@ -11482,7 +11482,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11508,7 +11508,7 @@ 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. - 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 sequence data @@ -11542,7 +11542,7 @@ In the examples above, a reagent is an operational component of a device, but th 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 + 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 @@ -11576,7 +11576,7 @@ In the examples above, a reagent is an operational component of a device, but th paraffin storage - a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term 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 @@ -11613,7 +11613,7 @@ In the examples above, a reagent is an operational component of a device, but th agar stab specimen - a specimen that is output of a process that cell culture inoculated into agar for long term storage. + 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 @@ -11629,7 +11629,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11653,7 +11653,7 @@ In the examples above, a reagent is an operational component of a device, but th Edinburgh score - A score that measures the dominance of a person's right or left hand in everyday activities. + 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 @@ -11691,7 +11691,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11705,7 +11705,7 @@ 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 - An objective which is fulfilled by the provision of some service e.g. a training service + An objective which is fulfilled by the provision of some service e.g. a training service Helen Parkinson OBI service provision objective @@ -11736,7 +11736,7 @@ 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. - The directed combination of a material entity with a specimen. + The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen @@ -11750,7 +11750,7 @@ In the examples above, a reagent is an operational component of a device, but th device creation objective - an objective which aims to create a device with a specified function + an objective which aims to create a device with a specified function PERSON: Helen Parkinson OBI device creation objective @@ -11764,7 +11764,7 @@ In the examples above, a reagent is an operational component of a device, but th 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. + 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 @@ -11808,7 +11808,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S agar stab storage - a storage process with input cell culture and agar and output agar stab for long time 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 @@ -11837,7 +11837,7 @@ 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 - A planned process that captures an image of an object. + A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition image creation @@ -11871,7 +11871,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S nucleic acid extract - An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + 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 @@ -11903,7 +11903,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S feature extraction - A planed process with objective of obtaining quantified values from an image. + A planed process with objective of obtaining quantified values from an image. PERSON: Jie Zheng MO_928: feature_extraction @@ -11930,7 +11930,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S array image acquisition - An image creation process that generate an image from the array. + An image creation process that generate an image from the array. PERSON: Jie Zheng array image acquisition MO_929: image_acquisition @@ -11946,7 +11946,7 @@ 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 - a function that allows specific identification of individual speciment from one another. + a function that allows specific identification of individual speciment from one another. EAGLE-I specimen fixation function @@ -11959,7 +11959,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S current amplification function - A current amplification function is an amplification function that increases the amplitude of a current. + A current amplification function is an amplification function that increases the amplitude of a current. EAGLE-I current amplification function @@ -11973,7 +11973,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S 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. + 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 @@ -11987,7 +11987,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S pump function - a transfer unction where the transfer requires work to move the entity, often against a gradient. + a transfer unction where the transfer requires work to move the entity, often against a gradient. EAGLE-I pump function @@ -12001,7 +12001,7 @@ 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. - is a transfer function that displaces cells from one place to another + is a transfer function that displaces cells from one place to another EAGLE-I cell transfer function @@ -12026,7 +12026,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S DNA extract - The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. + 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 @@ -12056,7 +12056,7 @@ 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 @@ -12154,7 +12154,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S 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. + 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 @@ -12371,7 +12371,7 @@ 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. - A measurement datum that describes the structural orientation of a material entity in 3D space. + 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 @@ -12384,7 +12384,7 @@ 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. + 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. @@ -12401,7 +12401,7 @@ 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. + 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 @@ -12415,7 +12415,7 @@ 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. + 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 @@ -12443,7 +12443,7 @@ 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. + 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 @@ -12458,7 +12458,7 @@ 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. + 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 @@ -12472,7 +12472,7 @@ 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. + 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 @@ -12486,7 +12486,7 @@ 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. + 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 @@ -12506,7 +12506,7 @@ 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 + 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 @@ -12530,7 +12530,7 @@ 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. + 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 @@ -12545,7 +12545,7 @@ 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. + 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 @@ -12565,7 +12565,7 @@ All subtype will be defined by textual definition now. half life datum (t 1/2) - The time it takes for 50% of a class of stochastic processes to occur. + The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters @@ -12580,7 +12580,7 @@ All subtype will be defined by textual definition now. 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. + 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 @@ -12618,7 +12618,7 @@ 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. - A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. + 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 @@ -12632,7 +12632,7 @@ All subtype will be defined by textual definition now. 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. + 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 @@ -12650,7 +12650,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12677,7 +12677,7 @@ 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) 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) @@ -12701,7 +12701,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12714,7 +12714,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 negative binding datum - A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. + A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. negative binding datum @@ -12746,7 +12746,7 @@ 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 + 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 @@ -12776,7 +12776,7 @@ 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) 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. + 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) @@ -12798,7 +12798,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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 + 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 @@ -12821,7 +12821,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific cytokine production by T cells - A process of cytokine production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -12846,7 +12846,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific tolerance induction by T cells - A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. + 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 @@ -12871,7 +12871,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12896,7 +12896,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific T cell activation - A process of T cell activation resulting from the recognition of a T cell epitope. + 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 @@ -12921,7 +12921,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -12946,7 +12946,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13007,7 +13007,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific T cell tolerance induction - A process of T cell tolerance induction resulting from the recognition of a T cell epitope. + 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 @@ -13032,7 +13032,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13057,7 +13057,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13082,7 +13082,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13107,7 +13107,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13147,7 +13147,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13172,7 +13172,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13243,7 +13243,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13268,7 +13268,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13307,7 +13307,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13332,7 +13332,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13387,7 +13387,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13427,7 +13427,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific RANTES production by T cells - A process of RANTES production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -13467,7 +13467,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13492,7 +13492,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13517,7 +13517,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13542,7 +13542,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13567,7 +13567,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 epitope specific cytotoxic T cell degranulation - A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. + 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 @@ -13606,7 +13606,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 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. + 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 @@ -13688,7 +13688,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) 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. + 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 @@ -13713,7 +13713,7 @@ 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 - A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. + 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 @@ -13738,7 +13738,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) 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. + 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 @@ -13763,7 +13763,7 @@ 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 - A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -13808,7 +13808,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13833,7 +13833,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13858,7 +13858,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13885,7 +13885,7 @@ 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 @@ -13910,7 +13910,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -13926,7 +13926,7 @@ 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 - An epitope specific immune intervention in which the induced response targets a T cell epitope + 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 @@ -13956,7 +13956,7 @@ 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. + 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 @@ -13970,7 +13970,7 @@ 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. + 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 @@ -13990,7 +13990,7 @@ 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. + 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 @@ -14024,7 +14024,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - 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). + 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 @@ -14046,7 +14046,7 @@ 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 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 @@ -14060,7 +14060,7 @@ 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. + 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 @@ -14102,7 +14102,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html cell collecting - A planned process that collects cells from culture. + A planned process that collects cells from culture. PERSON: Chris Stoeckert, Jie Zheng MO_982 harvest cell collecting @@ -14131,7 +14131,7 @@ 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. - A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. + 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 @@ -14151,7 +14151,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14167,7 +14167,7 @@ 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 - An epitope specific immune intervention in which the induced response targets a B cell 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 @@ -14182,7 +14182,7 @@ 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 enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. + 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 @@ -14196,7 +14196,7 @@ 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. + 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 @@ -14220,7 +14220,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14266,7 +14266,7 @@ 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. - The process in which a ligand binds to an MHC molecule to form a stable 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 @@ -14287,7 +14287,7 @@ 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. + 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 @@ -14308,7 +14308,7 @@ 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 + 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 @@ -14355,7 +14355,7 @@ 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. + 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 @@ -14370,7 +14370,7 @@ 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 @@ -14392,7 +14392,7 @@ 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. - 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. + 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 @@ -14418,7 +14418,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14444,7 +14444,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14470,7 +14470,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14504,7 +14504,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html 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. + 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 @@ -14527,7 +14527,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14543,7 +14543,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14582,7 +14582,7 @@ 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 - A service which has a material entity as specified input and/or specified output. + A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai @@ -14604,7 +14604,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14632,7 +14632,7 @@ 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. - A service that has some information content entity as input and output. + A service that has some information content entity as input and output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai @@ -14649,7 +14649,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14674,7 +14674,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14696,7 +14696,7 @@ 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 - A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) + 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) @@ -14717,7 +14717,7 @@ 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 - A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. + 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 @@ -14799,7 +14799,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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 + 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 @@ -14825,7 +14825,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14841,7 +14841,7 @@ 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. - A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) + 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) @@ -14856,7 +14856,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14873,7 +14873,7 @@ 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. - A scalar measurement datum that represents the number of events occuring over a time interval + A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum @@ -14898,7 +14898,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14920,7 +14920,7 @@ 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. - 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. + 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 @@ -14942,7 +14942,7 @@ 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. - 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. + 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 @@ -14972,7 +14972,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -14993,7 +14993,7 @@ 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 - A sequence data item that is about the primary structure of DNA + 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. @@ -15019,7 +15019,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15034,7 +15034,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15064,7 +15064,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15094,7 +15094,7 @@ 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. - A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. + 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 @@ -15109,7 +15109,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N binding A peptide binding to an MHC molecule to form a complex. - The process of material entities forming complexes. + 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 @@ -15131,7 +15131,7 @@ 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 - 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. + 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 @@ -15146,7 +15146,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15176,7 +15176,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N binding off rate measurement datum (koff) - A rate measurement datum of how quickly bound complexes disassociate + A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) @@ -15205,7 +15205,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N binding on rate measurement datum (kon) - A rate measurement datum of how quickly bound complexes form + A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) @@ -15229,7 +15229,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N 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. + 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 @@ -15568,7 +15568,7 @@ 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 - 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 + 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 @@ -15615,7 +15615,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 epitope specific granulysin production by T cells - A process of granulysin production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -15640,7 +15640,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 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. + 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 @@ -15661,7 +15661,7 @@ 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? @@ -15757,7 +15757,7 @@ 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. - a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). + 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 @@ -15771,7 +15771,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 immunoglobulin mediated histamine release - The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. + 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 @@ -15796,7 +15796,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific opsonization - opsonization resulting from antibody binding to epitope + 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 @@ -15821,7 +15821,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific immunoglobulin-mediated neutralization - immunoglobulin-mediated neutralization resulting from antibody binding to epitope + 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 @@ -15846,7 +15846,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific complement-dependent cytotoxicity - complement-dependent cytotoxicity resulting from antibody binding to epitope + 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 @@ -15871,7 +15871,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific antibody-dependent cellular cytotoxicity - antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope + 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 @@ -15893,7 +15893,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific immune complex formation - immune complex formation resulting from antibody binding to epitope + 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 @@ -15918,7 +15918,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific hypersensitivity - hypersensitivity resulting from antibody binding to epitope + 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 @@ -15943,7 +15943,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 B cell epitope specific histamine secretion mediated by immunoglobulin - histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope + 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 @@ -16018,7 +16018,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - An Investigation agent role borne by a person or organization which + An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group @@ -16043,7 +16043,7 @@ is realized in a specimen collection process. - A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16067,7 +16067,7 @@ is realized in a specimen collection process. - A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16091,7 +16091,7 @@ is realized in a specimen collection process. - A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16115,7 +16115,7 @@ is realized in a specimen collection process. - A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16139,7 +16139,7 @@ is realized in a specimen collection process. - A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16163,7 +16163,7 @@ is realized in a specimen collection process. - A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. + 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 @@ -16191,7 +16191,7 @@ is realized in a specimen collection process. Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. 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. - A planned process in which new information is inferred from existing information. + A planned process in which new information is inferred from existing information. drawing a conclusion @@ -16202,7 +16202,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A transcription profiling identification objective that aims to characterize the transcription start sites of genes. + A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective @@ -16225,7 +16225,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. + A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project @@ -16239,7 +16239,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A sequence feature identification objective that aims to characterize the interactions between protein and RNA. + A sequence feature identification objective that aims to characterize the interactions between protein and RNA. JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. Person: Jie Zheng Jie Zheng @@ -16279,7 +16279,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten secondary cultured cell - A cultured cell that has been passaged or derives from a cell that has been passaged in 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 @@ -16301,7 +16301,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten establishing cell line - a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). + a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush @@ -16328,7 +16328,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. + A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion). @@ -16385,7 +16385,7 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo - A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). + A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran @@ -16465,7 +16465,7 @@ PMID: 23587118. cultured immune cell population - a cultured cell population comprised of a single type of immune system cell + 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 @@ -16500,7 +16500,7 @@ PMID: 23587118. cell culture - A material entity comprised of cultured cells and the media in which they are being propagated or stored. + 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. @@ -16571,7 +16571,7 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. + A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at 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 examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush @@ -16601,7 +16601,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the principal investigator providing the specimens for the investigation + An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution @@ -16626,7 +16626,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center + An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution @@ -16674,7 +16674,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. - A plan specification which specifies the type of material that will be assayed in an investigation. + A plan specification which specifies the type of material that will be assayed in an investigation. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Material @@ -16703,7 +16703,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who is the contact representative of a Bioinformatics Resource Center + A person who is the contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact Name @@ -16736,7 +16736,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. - A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. + A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Scope @@ -16781,7 +16781,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that provides a service to store and distribute specimens + An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository @@ -16806,7 +16806,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the person who is contact representative of a Bioinformatics Resource Center + An email address of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email @@ -16835,7 +16835,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who is the contact representative at the sequencing facility + A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact Name @@ -16864,7 +16864,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who is a principal investigator and provides the specimen + A person who is a principal investigator and provides the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name @@ -16889,7 +16889,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the person collecting the specimen + An email address of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's email @@ -16924,7 +16924,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that provides sequence determination service + An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility @@ -16969,7 +16969,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype - An objective specification which indicates the type of data that will be generated and submitted to a database. + An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives @@ -16994,7 +16994,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the person collecting the specimen + An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution @@ -17019,7 +17019,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the contact representative at the sequencing facility + An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email @@ -17044,7 +17044,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A person who collects the specimen + A person who collects the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector Name @@ -17072,7 +17072,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of Project Method are Sequence, Array, Mass Spectrometry - A plan specification which indicates the assay type used to obtain data. + A plan specification which indicates the assay type used to obtain data. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Method @@ -17097,7 +17097,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An organization that is the affiliation of the contact representative at the sequencing facility + An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution @@ -17136,7 +17136,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A textual entity that is about any of the aspects of an investigation worth noting + A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments @@ -17188,7 +17188,7 @@ In regard to the statement that reagents are 'distinct' from the speci Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey - A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. + A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Capture @@ -17223,7 +17223,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A specimen identifier which is assigned by a specimen repository + A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID @@ -17258,7 +17258,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A specimen identifier which is assigned by a sequencing facility + A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility @@ -17307,7 +17307,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A sample preparation for assay that preparation of nucleic acids for a sequencing assay + A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method @@ -17332,7 +17332,7 @@ In regard to the statement that reagents are 'distinct' from the speci - An email address of the principal investigator providing the specimens for the investigation + An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's email @@ -17357,7 +17357,7 @@ In regard to the statement that reagents are 'distinct' from the speci - A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. + A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC @@ -17390,7 +17390,7 @@ In regard to the statement that reagents are 'distinct' from the speci secondary cultured cell population - A cultured cell population that is derived through one or more passages in culture. + A cultured cell population that is derived through one or more passages in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells 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 secondary cell culture sample @@ -17413,7 +17413,7 @@ In regard to the statement that reagents are 'distinct' from the speci cancer cell line - An immortal cell line derived from a transformed cell that was part of a malignant tumor. + An immortal cell line derived from a transformed cell that was part of a malignant tumor. cancer cell line @@ -17431,7 +17431,7 @@ In regard to the statement that reagents are 'distinct' from the speci 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 + 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 @@ -17443,7 +17443,7 @@ In regard to the statement that reagents are 'distinct' from the speci that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - An information content entity that expresses an assertion that is intended to be tested. + An information content entity that expresses an assertion that is intended to be tested. In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group hypothesis @@ -17472,7 +17472,7 @@ In regard to the statement that reagents are 'distinct' from the speci The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". - An information content entity that is inferred from data. + An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group @@ -17493,7 +17493,7 @@ The following are NOT conclusions based on data: data themselves; results from p primary cell culture - A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. + 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 @@ -17513,7 +17513,7 @@ The following are NOT conclusions based on data: data themselves; results from p cell line culture - A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently 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. @@ -17528,7 +17528,7 @@ The following are NOT conclusions based on data: data themselves; results from p 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. + 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 @@ -17571,7 +17571,7 @@ See Table 4 - A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. + A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. Chris Stoeckert, Jie Zheng LMA MLPA @@ -17588,7 +17588,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. + A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng Group: Penn Group DNA replication identification objective @@ -17601,7 +17601,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A molecular feature identification objective that aims to determine spatial organization of chromatin. + A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective @@ -17652,7 +17652,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A value specification that specifies the mass of some thing. + A value specification that specifies the mass of some thing. PERSON:Bjoern Peters mass value specification @@ -17664,7 +17664,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A value specification that is specifies one category out of a fixed number of nominal categories + A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification @@ -17688,7 +17688,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A value specification that consists of two parts: a numeral and a unit label + A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification @@ -17745,7 +17745,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A planned process in which predicted values for some thing are compared to measured values for that thing. + A planned process in which predicted values for some thing are compared to measured values for that thing. comparing prediction to measurement @@ -17757,7 +17757,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - An information content entity that specifies a value within a classification scheme or on a quantitative scale. + An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification @@ -17797,7 +17797,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. + an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. PERSON:Bjoern Peters predicted value @@ -17819,7 +17819,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - A predicted value where the prediction specifies the mass of some thing. + A predicted value where the prediction specifies the mass of some thing. PERSON:Bjoern Peters predicted mass value @@ -17846,7 +17846,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ 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 + 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 OBI developer call, 3-12-12 molecular-labeled material @@ -17913,7 +17913,7 @@ PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly + the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra weighted median item size @@ -17951,7 +17951,7 @@ PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. + N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html @@ -17965,7 +17965,7 @@ PMID: 23587118. - An organization that provides funding support for projects such as investigations. + An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group @@ -17982,7 +17982,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. + A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. PERSON: Jie Zheng, Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 NIAID GSCID-BRC @@ -18019,7 +18019,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. + A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC @@ -18053,7 +18053,7 @@ PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information + N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html @@ -18110,7 +18110,7 @@ PMID: 23587118. - A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. + A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group annotation provider @@ -18135,7 +18135,7 @@ PMID: 23587118. - A textual entity that is used to denote a sequence assembly. + A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group assembly name @@ -18150,7 +18150,7 @@ PMID: 23587118. - A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. + A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC @@ -18192,7 +18192,7 @@ PMID: 23587118. - A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. + A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. Person: Mathias Brochhausen, Jie Zheng WEB: http://en.wikipedia.org/wiki/Flash_freezing flash freezing @@ -18205,7 +18205,7 @@ PMID: 23587118. - A planned process with the objective to bring some material entity to a temperature below its freezing point. + A planned process with the objective to bring some material entity to a temperature below its freezing point. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing @@ -18219,7 +18219,7 @@ PMID: 23587118. competitive binding reference ligand role The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion. - A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. + A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. Bjoern Peters, Randi Vita, James A. Overton Bjoern Peters competitive binding reference ligand role @@ -18308,7 +18308,7 @@ PMID: 23587118. decision-theoretic analysis objective - An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. + An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. The best action to take is typically defined as the one that maximizes expected utility. PERSON: Bill Hogan decision analysis objective @@ -18445,7 +18445,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. + A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ Person:Chris Stoeckert PMID:15905473 @@ -18481,7 +18481,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.enzyme-linked antibody Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL). - A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. + A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. Bjoern Peters, Randi Vita, James A. Overton OBI enzyme-linked antibody @@ -18735,7 +18735,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 - A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. + A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ OBI developers @@ -18849,7 +18849,7 @@ https://www.doi.org/ - A cell specimen that contains only one cell. + A cell specimen that contains only one cell. Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl @@ -18880,7 +18880,7 @@ https://www.doi.org/ RNA Integrity Number calculation - A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. + A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. Chris Stoeckert, Bjoern Peters RIN calculation https://www.agilent.com/cs/library/applications/5989-1165EN.pdf @@ -18895,7 +18895,7 @@ https://www.doi.org/ RNA Integrity Number value specification - A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). + A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). Chris Stoeckert, Bjoern Peters RIN value specification OBI @@ -18924,7 +18924,7 @@ https://www.doi.org/ temperature value specification - A value specification that specifies the temperature of some thing. + A value specification that specifies the temperature of some thing. Chris Stoeckert OBI temperature value specification @@ -18952,7 +18952,7 @@ https://www.doi.org/ volume value specification - A value specification that specifies the volume of some thing. + A value specification that specifies the volume of some thing. Chris Stoeckert OBI volume value specification @@ -18982,7 +18982,7 @@ https://www.doi.org/ courier organization - An organization that delivers messages, packages, and mail. + An organization that delivers messages, packages, and mail. Chris Stoeckert, Helena Ellis courier https://en.wikipedia.org/wiki/Courier @@ -18998,7 +18998,7 @@ https://www.doi.org/ courier tracking number - A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. + A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -19013,7 +19013,7 @@ https://www.doi.org/ tissue section thickness - A length measurement datum that is the result of an assay measuring the thickness of a tissue section. + A length measurement datum that is the result of an assay measuring the thickness of a tissue section. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB @@ -19050,7 +19050,7 @@ https://www.doi.org/ molecular analysis facility organization An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. - An organization that provides molecular analysis service. + An organization that provides molecular analysis service. Chris Stoeckert, Helena Ellis MAF NCI BBRB, OBIB @@ -19070,7 +19070,7 @@ https://www.doi.org/ - A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. + A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 @@ -19083,7 +19083,7 @@ https://www.doi.org/ - 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. + 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 @@ -19097,7 +19097,7 @@ https://www.doi.org/ - An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. + An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. Rebecca Jackson DSH differential screening @@ -19165,7 +19165,7 @@ https://www.doi.org/ defined population inclusion criterion inclusion based on age, sex, and living region (rural area or specified city). - An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. + An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. Chris Stoeckert, Mathias Brochhausen MIABIS 2.0 https://github.com/obi-ontology/obi/issues/920 @@ -19251,7 +19251,7 @@ https://www.doi.org/ age since culture seeding measurement datum - An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). + An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). Stephen A. Fisher, Junhyong Kim, Dan Berrios age of culture age since culture seeding measurement datum @@ -19553,7 +19553,7 @@ https://www.doi.org/ "18-33 years old" - An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. + An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen https://github.com/obi-ontology/obi/issues/839 age group inclusion criterion @@ -19667,7 +19667,7 @@ https://www.doi.org/ 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. + 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 @@ -19683,7 +19683,7 @@ https://www.doi.org/ RNA extraction with polyA depletion - A RNA extraction process in which only RNAs lacking a polyA tail are retained + 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 @@ -19697,7 +19697,7 @@ https://www.doi.org/ machine learning - A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. + A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. Mark A. Miller https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN @@ -19711,7 +19711,7 @@ 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://github.com/TrisSN @@ -19725,7 +19725,7 @@ 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://github.com/TrisSN @@ -19738,7 +19738,7 @@ https://www.doi.org/ - 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. + 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 @@ -19759,7 +19759,7 @@ https://www.doi.org/ swab specimen - A specimen that is stored on a swab as the output of a collecting specimen with swab process. + A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI https://github.com/obi-ontology/obi/issues/910 @@ -19775,7 +19775,7 @@ https://www.doi.org/ collecting specimen with swab - A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). + A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 @@ -19790,7 +19790,7 @@ https://www.doi.org/ 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. + 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 @@ -19803,7 +19803,7 @@ https://www.doi.org/ 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. + An information content entity that contains information about a nationwide group of individuals. MIABIS Sarah Bost MIABIS contributors @@ -19817,7 +19817,7 @@ https://www.doi.org/ 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. + 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 @@ -19832,7 +19832,7 @@ https://www.doi.org/ Site-directed mutagenesis was used to prepare mutants of the Hypoxia-inducible factor-1 (HIF-1) alpha subunit to investigate the role of certain amino acids in hypoxia. (PMID:12393189) - An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. + An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. Rebecca Jackson url:https://www.ncbi.nlm.nih.gov/books/NBK21945/ https://github.com/obi-ontology/obi/issues/1058 @@ -19847,7 +19847,7 @@ https://www.doi.org/ Error-prone PCR was used to introduce amino acid mutations to the cAMP receptor protein (CRP) of E. coli to investigate strain engineering to improve osmotolerance for industrial requirements. (PMID:22179860) - An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. + An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. Rebecca Jackson PMID:15153637 https://github.com/obi-ontology/obi/issues/1058 @@ -19861,7 +19861,7 @@ https://www.doi.org/ - A genetic transformation which reduces the expression of a specific gene or genes in an organism. + A genetic transformation which reduces the expression of a specific gene or genes in an organism. Rebecca Jackson gene knock-down url:https://en.wikipedia.org/wiki/Gene_knockdown @@ -19881,7 +19881,7 @@ https://www.doi.org/ - A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. + A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. Rebecca Jackson RNA interference gene knockdown url:https://en.wikipedia.org/wiki/Gene_knockdown @@ -19897,7 +19897,7 @@ 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. - An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). + 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 @@ -19916,7 +19916,7 @@ https://www.doi.org/ - A specimen composed of an individual organism to be studied in an investigation. + 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 @@ -19931,7 +19931,7 @@ https://www.doi.org/ 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 @@ -19948,7 +19948,7 @@ https://www.doi.org/ - A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). + A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). Jie Zheng short interspersed elements PCR PMID: 12711348 @@ -19964,7 +19964,7 @@ https://www.doi.org/ - 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. + 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 @@ -19981,7 +19981,7 @@ https://www.doi.org/ - An electrophoresis that separates and characterize proteins based on reaction with antibodies. + An electrophoresis that separates and characterize proteins based on reaction with antibodies. Jie Zheng IEP https://en.wikipedia.org/wiki/Immunoelectrophoresis @@ -19997,7 +19997,7 @@ https://www.doi.org/ - 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. + 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 @@ -20012,7 +20012,7 @@ https://www.doi.org/ - 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. + 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 @@ -20028,7 +20028,7 @@ https://www.doi.org/ - 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. + 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 @@ -20044,7 +20044,7 @@ https://www.doi.org/ - An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. + 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 @@ -20059,7 +20059,7 @@ https://www.doi.org/ - An organism feature identification objective that aims to detect insecticide resistance of an insect. + 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 @@ -20075,7 +20075,7 @@ https://www.doi.org/ 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. + 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 @@ -20183,7 +20183,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - A categorical value specification in which the available categories were created with an explicit order. + A categorical value specification in which the available categories were created with an explicit order. https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet. @@ -20249,7 +20249,7 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - An ordinal value specification that indicates that either + An ordinal value specification that indicates that either a) an analyte or mesaurand is present in an evaluant, or b) that the amount of analyte/measurand detected is over some predetermined threshold. Mark Andrew Miller, ORCID:0000-0001-9076-6066 @@ -20287,7 +20287,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - 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. + 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 @@ -20300,7 +20300,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - 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. + 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 @@ -20313,7 +20313,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. + 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 @@ -20327,7 +20327,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre surveillance process - An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. + An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. Chris Stoeckert Shane Babcock, OBI https://github.com/obi-ontology/obi/issues/1181 @@ -20343,7 +20343,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cluster study group role A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound. - A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. + A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. Chris Stoeckert, Brianna Lindsay cluster study arm ClinEpiDB @@ -20358,7 +20358,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre compound study group role A compound study group consisting of geographically proximate households that share a common water source. - A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. + A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. Chris Stoeckert, Brianna Lindsay compound study arm ClinEpiDB @@ -20372,7 +20372,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre altitude measurement datum - A length measurement datum between a point at sea or ground level and some point above it. + A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum @@ -20386,7 +20386,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre duration of specimen collection Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration. - A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. + A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. specimen collection duration VEuPathDB specimen collection duration @@ -20415,7 +20415,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre material supplier - A person or organization that provides material supplies to other people or organizations. + A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier @@ -20429,7 +20429,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre prevalence of pathogen in specimens prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR - A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. + A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. Chris Stoeckert prevalence of pathogen VEuPathDB @@ -20444,7 +20444,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre prevalence of blood meal specimens from a host organism prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal. - A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. + A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. Chris Stoeckert host blood index VEuPathDB @@ -20459,7 +20459,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre presence of blood from host organism in blood meal specimen presence of blood meal host organism indicated by boolean values of yes or no. - A data item that indicates whether blood in a blood meal specimen came from a specified host organism. + A data item that indicates whether blood in a blood meal specimen came from a specified host organism. Chris Stoeckert presence of blood meal host organism VEuPathDB @@ -20483,7 +20483,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood meal source organism - An organism that is the source of a blood meal. + An organism that is the source of a blood meal. Chris Stoeckert blood meal host organism VEuPathDB @@ -20498,7 +20498,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood meal source role A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal. - A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. + A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. Will deprecate this term in VEuPathDB ontology once in OBI. Chris Stoeckert http://purl.obolibrary.org/obo/EUPATH_0000791 @@ -20511,7 +20511,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A role of a material entity realized in drawing an arthropod in the direction of the material. + A role of a material entity realized in drawing an arthropod in the direction of the material. John Judkins attractant IRO:0000034 @@ -20526,7 +20526,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. + An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 @@ -20540,7 +20540,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that has the objective of collecting gravid female arthropods. + An arthropod specimen collection process that has the objective of collecting gravid female arthropods. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 @@ -20554,7 +20554,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. + An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. John Judkins VSMO:0000514 https://github.com/obi-ontology/obi/issues/1302 @@ -20568,7 +20568,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection by aspiration that occurs in the daytime. + An arthropod specimen collection by aspiration that occurs in the daytime. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 @@ -20582,7 +20582,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection by aspiration that catches specimens resting inside a human house. + An arthropod specimen collection by aspiration that catches specimens resting inside a human house. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB @@ -20595,7 +20595,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An arthropod specimen collection process that occurs while the arthropods land on a surface. + An arthropod specimen collection process that occurs while the arthropods land on a surface. John Judkins collection of landing insects VSMO:0001457 @@ -20610,7 +20610,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. + An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB @@ -20630,7 +20630,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre barcode target locus role - An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. + An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 @@ -20650,7 +20650,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre oligonucleotide primer set - A processed material that consists of oligonucleotides that bear a primer role. + A processed material that consists of oligonucleotides that bear a primer role. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 @@ -20663,7 +20663,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A data item that is about resistance to an insecticide. + A data item that is about resistance to an insecticide. John Judkins VEuPathDB insecticide resistance datum @@ -20685,7 +20685,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A data item that is the specified output of an organism detection assay. + A data item that is the specified output of an organism detection assay. John Judkins VEuPathDB organism detection datum @@ -20697,7 +20697,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. + A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system @@ -20710,7 +20710,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. + A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system @@ -20723,7 +20723,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Organization that undertakes a clinical study at some point in time. + Organization that undertakes a clinical study at some point in time. Chris Stoeckert Cristian Cocos Jie Zheng @@ -20737,7 +20737,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. + A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. John Judkins VEuPathDB sequencing protocol @@ -20755,7 +20755,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A protocol that specifies processes to fulfill a specimen collection objective. + A protocol that specifies processes to fulfill a specimen collection objective. John Judkins VEuPathDB specimen collection protocol @@ -20783,7 +20783,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A symbol that denotes a participant under investigation. + A symbol that denotes a participant under investigation. John Judkins VEuPathDB participant identifier @@ -20795,7 +20795,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A temperature measurement datum that is about an axilla. + A temperature measurement datum that is about an axilla. John Judkins VEuPathDB axillary temperature measurement datum @@ -20807,7 +20807,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A temperature measurement datum that is about an organism. + A temperature measurement datum that is about an organism. Chris Stoeckert Jie Zheng Penn Group @@ -20826,7 +20826,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - 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 @@ -20838,7 +20838,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An age since birth measurement datum at the time of subject enrollment. + An age since birth measurement datum at the time of subject enrollment. Jie Zheng Penn Group age since birth at time of enrollment @@ -20850,7 +20850,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An age since birth measurement datum at the time of a clinical visit. + An age since birth measurement datum at the time of a clinical visit. Chris Stoeckert Grant Dorsey Jie Zheng @@ -20865,7 +20865,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A data item that is about a collection of insects. + A data item that is about a collection of insects. John Judkins entomological measurement datum VEuPathDB @@ -20878,7 +20878,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A scalar measurement datum that is the result of measuring temperature. + A scalar measurement datum that is the result of measuring temperature. John Judkins VEuPathDB temperature measurement datum @@ -20891,7 +20891,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre extraction date - A time measurement datum that specifies when some material was extracted from an input material. + 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 @@ -20905,7 +20905,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre extraction duration time - A time measurement datum that is the result of measuring the duration of an extraction process. + 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 @@ -20919,7 +20919,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -20933,7 +20933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -20947,7 +20947,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre laboratory postal address - A postal address used as a directive to deliver something to a laboratory. + 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 @@ -20963,7 +20963,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -20989,7 +20989,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A complex of molecular entitites which is the result of an antibody binding to an antigen. + A complex of molecular entitites which is the result of an antibody binding to an antigen. Bjoern Peters Hector Guzman-Orozco IEDB @@ -21015,7 +21015,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope 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 @@ -21034,7 +21034,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A complex of molecular entities which is the result of a MHC molecule binding with a ligand. + A complex of molecular entities which is the result of a MHC molecule binding with a ligand. Bjorne Peters Hector Guzman-Orozco IEDB @@ -21048,7 +21048,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21062,7 +21062,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21077,7 +21077,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21090,7 +21090,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21104,7 +21104,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21120,7 +21120,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21134,7 +21134,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21149,7 +21149,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21162,7 +21162,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21175,7 +21175,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21188,7 +21188,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -21203,7 +21203,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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/ @@ -21222,7 +21222,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A binding datum that is expressed as a categorical value. + A binding datum that is expressed as a categorical value. IEDB qualitative binding datum IEDB @@ -21235,7 +21235,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A binding datum that is expressed using numbers. + A binding datum that is expressed using numbers. IEDB IEDB quantitative binding datum @@ -21262,7 +21262,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). + A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). Bjoern Peters Hector Guzman-Orozco IEDB @@ -21290,7 +21290,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). + A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). Bjoern Peters Hector Guzman-Orozco IEDB @@ -21309,7 +21309,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A blood harvesting process in which white blood cells are separated from a blood specimen. + 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 @@ -21321,7 +21321,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences. + An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences. Christian Stoeckert ORCID:0000-0002-5714-991X Jie Zheng ORCID:0000-0002-2999-0103 laboratory @@ -21338,7 +21338,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. + 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 @@ -21361,7 +21361,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of perforin during cytotoxic T cell degranulation. + The release of perforin during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21384,7 +21384,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of granzyme A during cytotoxic T cell degranulation. + The release of granzyme A during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21407,7 +21407,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of granzyme B during cytotoxic T cell degranulation. + The release of granzyme B during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21430,7 +21430,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The release of granulysin during cytotoxic T cell degranulation. + The release of granulysin during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters @@ -21453,7 +21453,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The subject being scanned in an MRI study, and bearor of data derived from that study. + The subject being scanned in an MRI study, and bearor of data derived from that study. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" @@ -21479,7 +21479,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role. + An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" @@ -21495,7 +21495,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The NMR/MRI machine protocol about the radiofrequency pulse sequence. + The NMR/MRI machine protocol about the radiofrequency pulse sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" @@ -21515,7 +21515,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. + A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 organism diagnostic process @@ -21533,7 +21533,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. + A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 diagnosis of an organism @@ -21556,7 +21556,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. + A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific XCL1 release by T cells @@ -21614,7 +21614,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. + A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. The Mother and Child Health and Education Trust mid-upper arm circumference datum @@ -21667,7 +21667,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - The administration of a malignant cell to a host. + The administration of a malignant cell to a host. Hector Guzman-Orozco IEDB tumor challenge @@ -21679,7 +21679,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A preparative chromatography in which material components are separated in a liquid solution. + A preparative chromatography in which material components are separated in a liquid solution. Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1685 @@ -21692,7 +21692,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay. + A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay. Bjoern Peters Hector Guzman-Orozco OBI @@ -21706,7 +21706,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay. + A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay. Bjoern Peters Hector Guzman-Orozco OBI @@ -21733,7 +21733,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Staining using carboxyfluorescein succinimidyl ester. + Staining using carboxyfluorescein succinimidyl ester. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 carboxyfluorescein succinimidyl ester staining @@ -21745,7 +21745,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Staining using Annexin V to detect apoptotic cells. + Staining using Annexin V to detect apoptotic cells. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 Annexin V staining @@ -21763,7 +21763,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. + A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. Sebastian Duesing CADI chronic allograft damage index score @@ -21775,7 +21775,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies the degree of function of a critically ill patient's organs. + A clinical data item that quantifies the degree of function of a critically ill patient's organs. Sebastian Duesing SOFA score https://en.wikipedia.org/wiki/SOFA_score @@ -21794,7 +21794,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. + A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. Sebastian Duesing MD global, PGA physician's global assessment of disease activity @@ -21806,7 +21806,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. + A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. Sebastian Duesing HLA mismatch count, HLA mismatch human leukocyte antigen mismatch count @@ -21829,7 +21829,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An objective specification that is fulfilled by reducing the severity of a disease in a particular organism. + An objective specification that is fulfilled by reducing the severity of a disease in a particular organism. Sebastian Duesing disease severity reduction objective @@ -21840,7 +21840,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An objective specification that is fulfilled by preventing the development of a disease in a particular organism. + An objective specification that is fulfilled by preventing the development of a disease in a particular organism. Sebastian Duesing disease prevention objective @@ -21874,7 +21874,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms. + An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms. Sebastian Duesing disease prevalence reduction objective @@ -21917,7 +21917,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A purification to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC protein complex, while others contain impurities and are not of interest. + A purification to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC protein complex, while others contain impurities and are not of interest. Randi Vita Sebastian Duesing antibody purification of MHC protein complex @@ -21929,7 +21929,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. + A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. Sebastian Duesing https://pubmed.ncbi.nlm.nih.gov/7636775/ DOI: 10.1016/0022-3999(94)00125-o multidimensional fatigue inventory score @@ -21952,7 +21952,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre albumin-free serum - A blood serum specimen that contains no albumin. + A blood serum specimen that contains no albumin. Sebastian Duesing https://github.com/obi-ontology/obi/issues/493 Philippe Rocca-Serra @@ -21989,7 +21989,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre fasting Pre-test fasting is required or recommended for several blood tests, including glucose and C-peptide tests. 8–12 hours is typical for fasting duration. - A planned process in which an organism drinks only water and does not eat for a specified period of time. + A planned process in which an organism drinks only water and does not eat for a specified period of time. Sebastian Duesing A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. https://github.com/obi-ontology/obi/issues/494 @@ -22004,7 +22004,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Overnight fasting commonly occurs prior to a blood draw scheduled in the morning. - A fasting with a duration of 8–12 hours, typically occurring overnight. + A fasting with a duration of 8–12 hours, typically occurring overnight. Sebastian Duesing A.M. Simundic et al., Standardization of collection requirements for fasting samples: For the Working Group on Preanalytical Phase (WG-PA) of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Clinica Chimica Acta, Volume 432, 2014, Pages 33-37, ISSN 0009-8981, https://doi.org/10.1016/j.cca.2013.11.008. https://github.com/obi-ontology/obi/issues/494 @@ -22024,7 +22024,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats. + An organismal quality that inheres in an organism that has completed a fasting process, and which ceases to inhere in that organism once that organism drinks a liquid other than water or eats. Sebastian Duesing https://github.com/obi-ontology/obi/issues/494 Philippe Rocca-Serra @@ -22056,7 +22056,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument. + An information content entity that indicates the smallest increment that can be resolved on the scale of a measurement instrument. Sebastian Duesing least count https://en.wikipedia.org/wiki/Least_count @@ -22073,7 +22073,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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. + 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 @@ -22398,7 +22398,7 @@ This issue is outside the scope of OBI. 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 cell culture sample @@ -22436,7 +22436,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from 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.' consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. PERSON:Matthew Brush @@ -22591,7 +22591,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ glucose in solution Glucose present in blood - A scattered aggregate of glucose molecules in a liquid + A scattered aggregate of glucose molecules in a liquid PERSON: Jie Zheng glucose molecules glucose in solution @@ -22682,7 +22682,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ geometric mean calculation - A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). + A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). Mathias Brochhausen PERSON: Mathias Brochhausen A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). @@ -23313,7 +23313,7 @@ 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 + 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 @@ -23334,7 +23334,7 @@ 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 - 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 + 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 @@ -23355,7 +23355,7 @@ 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 - Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method + 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 @@ -23416,7 +23416,7 @@ 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) - 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 @@ -23599,7 +23599,7 @@ 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) - 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 @@ -23939,7 +23939,7 @@ 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 - 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 @@ -24039,7 +24039,7 @@ 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 @@ -24272,7 +24272,7 @@ allows correct classification of FWER dt survival analysis objective 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 + 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 @@ -24294,7 +24294,7 @@ 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 @@ -24332,7 +24332,7 @@ 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) + 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 @@ -24353,7 +24353,7 @@ allows correct classification of FWER dt 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 + 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. @@ -24371,7 +24371,7 @@ allows correct classification of FWER dt 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. + a data transformation objective of determining the concordance or agreement between human judges. Person:Alan Ruttenberg Person:Helen Parkinson inter-rater agreement @@ -24405,7 +24405,7 @@ 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 @@ -24480,7 +24480,7 @@ 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 is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. + 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 @@ -24692,7 +24692,7 @@ 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 @@ -25400,7 +25400,7 @@ information_encoding 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. + 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 @@ -25509,7 +25509,7 @@ 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. - 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. + 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 @@ -25530,7 +25530,7 @@ information_encoding 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). + 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 @@ -25550,7 +25550,7 @@ information_encoding 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. + 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 @@ -25570,7 +25570,7 @@ information_encoding 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. + 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 @@ -25653,7 +25653,7 @@ 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. + 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 @@ -25682,7 +25682,7 @@ 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' + 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 @@ -25703,7 +25703,7 @@ 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. + 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 @@ -25736,7 +25736,7 @@ 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 @@ -25769,7 +25769,7 @@ 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. + 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 @@ -25798,7 +25798,7 @@ 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). + 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 @@ -26024,7 +26024,7 @@ to create a common base for comparisons. 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. + 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 @@ -26090,7 +26090,7 @@ 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 - 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 @@ -26162,7 +26162,7 @@ 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 - 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 @@ -26313,7 +26313,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26338,7 +26338,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26370,7 +26370,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26402,7 +26402,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26422,7 +26422,7 @@ class labels for these objects. The resulting predictor can be used to attach cl survival analysis data transformation - A data transformation which has the objective of performing survival analysis. + A data transformation which has the objective of performing survival analysis. James Malone PERSON: James Malone survival analysis data transformation @@ -26442,7 +26442,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26459,7 +26459,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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. + 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 @@ -26473,7 +26473,7 @@ 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 - is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. + 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 @@ -26493,7 +26493,7 @@ class labels for these objects. The resulting predictor can be used to attach cl 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 @@ -26516,7 +26516,7 @@ determinations of compounds. 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. + 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 @@ -26530,7 +26530,7 @@ determinations of compounds. ANOVA - A statistical hypothesis test in which the means of several groups are all equal. + A statistical hypothesis test in which the means of several groups are all equal. James Malone ANOVA @@ -26630,7 +26630,7 @@ 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 - a role which inheres in some molecular entity realized during the process of buffering + a role which inheres in some molecular entity realized during the process of buffering Person:Helen Parkinson Person:Philippe Rocca-Serra buffer @@ -26779,7 +26779,7 @@ 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. - An 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. + An 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 @@ -26803,7 +26803,7 @@ 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 - a role that borne by an organism and realized by some group randomization process + a role that borne by an organism and realized by some group randomization process Person:Helen Parkinson Philippe Rocca-Serra randomized group participant role @@ -26895,7 +26895,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 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 + 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 @@ -26916,7 +26916,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 edited document The OBI manuscript is (much) edited imformation - A document which is the output of a document editing process + A document which is the output of a document editing process Person:Bjoern Peters Philippe Rocca-Serra edited document @@ -26947,7 +26947,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 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 + A material entity that has been going through a process of being put into solution Person:Bjoern Peters Philippe Rocca-Serra dissolved material entity @@ -26968,7 +26968,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 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 @@ -27699,7 +27699,7 @@ 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. + 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 @@ -28102,7 +28102,7 @@ defines and states the requirements (positive or negative) for an entity to be c 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. + 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: @@ -28776,7 +28776,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ 'establishing cell culture' - a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). + a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. @@ -30070,7 +30070,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30084,7 +30084,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30098,7 +30098,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30295,7 +30295,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30310,7 +30310,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30354,7 +30354,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30369,7 +30369,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30384,7 +30384,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30419,7 +30419,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30434,7 +30434,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30448,7 +30448,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30462,7 +30462,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30507,7 +30507,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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 @@ -30531,7 +30531,7 @@ Possible ecological risks of transgenic organism release when transgenes affect 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. @@ -30559,7 +30559,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30629,7 +30629,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30668,7 +30668,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30721,7 +30721,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30760,7 +30760,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30807,7 +30807,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -30934,7 +30934,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31251,7 +31251,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31287,7 +31287,7 @@ 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. - 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 @@ -31322,7 +31322,7 @@ 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. - 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 @@ -31344,7 +31344,7 @@ 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. - A material entity that is added to another material entity in an “adding a material entity into a target” process. + A material entity that is added to another material entity in an “adding a material entity into a target” 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 @@ -31366,7 +31366,7 @@ 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. - A material entity that receives the addition of another material entity in an “adding a material entity into a target” process. + A material entity that receives the addition of another material entity in an “adding a material entity into a target” 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 @@ -31394,7 +31394,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31424,7 +31424,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31438,7 +31438,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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 @@ -31739,7 +31739,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it allergen Birch pollen is an allergen - A material entity bearing the disposition to cause an allergic reaction + A material entity bearing the disposition to cause an allergic reaction IEDB IEDB allergen @@ -31852,7 +31852,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it 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) + 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 @@ -31868,7 +31868,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ - A specimen that has been fixed in formalin and embedded in paraffin. + A specimen that has been fixed in formalin and embedded in paraffin. MIABIS formalin-fixed paraffin-embeded specimen @@ -32520,7 +32520,7 @@ realizes some 'host of immune response role' GenePattern module SVM - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + 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 @@ -32566,7 +32566,7 @@ realizes some 'host of immune response role' GenePattern module KMeansClustering - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + 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 @@ -32592,7 +32592,7 @@ realizes some 'host of immune response role' 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 is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation @@ -32603,7 +32603,7 @@ realizes some 'host of immune response role' 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. + 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 @@ -32628,7 +32628,7 @@ realizes some 'host of immune response role' GenePattern module KNN - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN @@ -32641,7 +32641,7 @@ realizes some 'host of immune response role' GenePattern module HierarchicalClustering - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + 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 @@ -32666,7 +32666,7 @@ realizes some 'host of immune response role' GenePattern module PCA - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + 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 @@ -32691,7 +32691,7 @@ realizes some 'host of immune response role' GenePattern HeatMapViewer data visualization - The GenePattern process of generating Heat Maps from clustered data. + The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization @@ -32703,7 +32703,7 @@ realizes some 'host of immune response role' GenePattern HierarchicalClusteringViewer data visualization - The GenePattern process of generating hierarchical clustering visualization from clustered data. + The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization @@ -32716,7 +32716,7 @@ realizes some 'host of immune response role' GenePattern module HeatMapViewer - A GenePattern software module which is used to generate a heatmap view of data. + A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer @@ -32729,7 +32729,7 @@ realizes some 'host of immune response role' GenePattern module HierarchicalClusteringViewer - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer