From 851d85277974210431adb2fc17754bc2d7a02ad4 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 18 Jun 2024 12:51:03 -0700 Subject: [PATCH 1/2] Making all definitions language tagged. Fixes #1793 --- 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 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 From 8565b698f52ac6cac2cfbeb2a7176fa64115e8f8 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 20 Jun 2024 11:18:42 -0700 Subject: [PATCH 2/2] Changing templates to use @en --- src/ontology/templates/biobank-specimens.tsv | 2 +- src/ontology/templates/biopsy.tsv | 2 +- src/ontology/templates/devices.tsv | 2 +- src/ontology/templates/epitope-assays.tsv | 2 +- src/ontology/templates/obsolete.tsv | 2 +- src/ontology/templates/organizations.tsv | 2 +- src/ontology/templates/sample-collection.tsv | 2 +- src/ontology/templates/specimen-assay-data.tsv | 2 +- src/ontology/templates/study-designs.tsv | 2 +- src/ontology/templates/value-specifications.tsv | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv index 40c3371d..b3acd9e5 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 %)) +ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 %)) 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..9420768f 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 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/devices.tsv b/src/ontology/templates/devices.tsv index 9e1b4426..79740487 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 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..f832e9a1 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 termAL 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 %) 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/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 3cb52b68..cfc78915 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 termAL 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 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..1d157537 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 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/sample-collection.tsv b/src/ontology/templates/sample-collection.tsv index 2248c9d2..e3320109 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 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/specimen-assay-data.tsv b/src/ontology/templates/specimen-assay-data.tsv index 6b48dbdd..4cc2da3a 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 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..f1debcfd 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 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..fe5844bb 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 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