Ontology for Biomedical Investigations
type: Ontology
version IRI: obi.owl
default language: en
OBO foundry unique label: Ontology for Biomedical Investigations
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
creator: Chris Stoeckert
creator: Chris Taylor
creator: Christian Bolling
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James A. Overton
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
creator: Philippe Rocca-Serra
creator: Phillip Lord
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
date: 2009-07-31
description: An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.
Format: OWL-DL
subject: An ontology for the annotation of biomedical and functional genomics experiments.
license: http://creativecommons.org/licenses/by/4.0/
comment: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
version info: 2025-05-01

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred label
editor preferred term: editor preferred term
editor preferred term: editor preferred term~editor preferred label
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred label
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred term: example of usage
has curation status: IAO_0000122
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred term: definition
editor preferred term: textual definition
has curation status: IAO_0000122
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: IAO_0000122
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: IAO_0000122
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred term: alternative label
has curation status: IAO_0000125
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative term

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: IAO_0000122
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred term: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
editor preferred term: ontology term requester
has curation status: IAO_0000125
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

is denotator type
type: AnnotationProperty
editor preferred term: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred term: imported from
has curation status: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
term editor: PERSON:Alan Ruttenberg

antisymmetric property
type: AnnotationProperty
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg
sub property of: logical characteristic of object property

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
has curation status: IAO_0000125
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred term: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred term: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred term: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred term: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred term: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred term: is allocated id range
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has ontology root term
type: AnnotationProperty
editor preferred term: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred term: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred term: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
has curation status: IAO_0000125
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

ISA alternative term
type: AnnotationProperty
editor preferred term: ISA alternative term
has curation status: IAO_0000122
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
term editor: Person: Alejandra Gonzalez-Beltran
term editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative label

NIAID GSCID-BRC alternative term
type: AnnotationProperty
editor preferred term: NIAID GSCID-BRC alternative term
has curation status: IAO_0000122
definition: 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).
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
sub property of: alternative label

IEDB alternative term
type: AnnotationProperty
editor preferred term: IEDB alternative term
has curation status: IAO_0000122
definition: An alternative term used by the IEDB.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative label

FGED alternative term
type: AnnotationProperty
editor preferred term: FGED alternative term
has curation status: IAO_0000122
definition: An alternative term used by the Functional Genomics Data (FGED) Society.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: Penn Group
sub property of: alternative label

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

defined by construct
type: AnnotationProperty
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
Contributor: https://orcid.org/0000-0002-7356-1779
Contributor: https://orcid.org/0000-0002-8688-6599

abbreviation
type: AnnotationProperty
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initalisms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

ambiguous synonym
type: AnnotationProperty
definition: A synonym type for describing ambiguous synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

dubious synonym
type: AnnotationProperty
definition: A synonym type for describing dubious synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

layperson synonym
type: AnnotationProperty
example of usage: EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
definition: A synonym type for describing layperson or colloquial synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

plural form
type: AnnotationProperty
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
definition: A synonym type for describing pluralization synonyms
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

UK spelling synonym
type: AnnotationProperty
example of usage: CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
definition: A synonym type for describing UK spelling variants
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

misspelling
type: AnnotationProperty
definition: A synonym type for common misspellings
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/132
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

misnomer
type: AnnotationProperty
definition: A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/133
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

previous name
type: AnnotationProperty
example of usage: MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
definition: A synonym type for names that have been used as primary labels in the past.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/139
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-07-25
sub property of: SynonymTypeProperty

legal name
type: AnnotationProperty
example of usage: The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
definition: A synonym type for the legal entity name
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/141
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-07-27
sub property of: SynonymTypeProperty

International Nonproprietary Name
type: AnnotationProperty
example of usage: CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label
definition: The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/149
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-09-30
has exact synonym: INN
sub property of: SynonymTypeProperty

latin term
type: AnnotationProperty
example of usage: nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis
definition: A synonym type for describing Latin term synonyms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/146
contributor: https://orcid.org/0000-0002-1773-2692
created: 2023-10-12
sub property of: SynonymTypeProperty

acronym
type: AnnotationProperty
example of usage: NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
definition: A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/135
contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-11-01
sub property of: SynonymTypeProperty

has symbol
type: AnnotationProperty
example of usage: A serial number such as "12324X"; a stop sign; a written proper name such as "OBI
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/144
contributor: https://orcid.org/0000-0002-6523-4866
created: 2024-03-25

Contributor
type: AnnotationProperty
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
comment: An entity responsible for making contributions to the content of the resource.

Coverage
type: AnnotationProperty
description: Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
comment: The extent or scope of the content of the resource.

Creator
type: AnnotationProperty
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
comment: An entity primarily responsible for making the content of the resource.

Date
type: AnnotationProperty
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
comment: An account of the content of the resource.

Format
type: AnnotationProperty
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
comment: The physical or digital manifestation of the resource.

Resource Identifier
type: AnnotationProperty
description: Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
comment: An unambiguous reference to the resource within a given context.

Language
type: AnnotationProperty
description: Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.
comment: A language of the intellectual content of the resource.

Publisher
type: AnnotationProperty
description: Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.
comment: An entity responsible for making the resource available

Relation
type: AnnotationProperty
description: Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a related resource.

Rights Management
type: AnnotationProperty
description: Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
comment: Information about rights held in and over the resource.

Source
type: AnnotationProperty
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
comment: The topic of the content of the resource.

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

Resource Type
type: AnnotationProperty
description: Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
comment: The nature or genre of the content of the resource.

license
type: AnnotationProperty
term editor: Mark Miller
date: 2018-05-11T13:47:29Z

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
sub property of: alternative label

has cross-reference
type: AnnotationProperty
example of usage: disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/123
contributor: https://orcid.org/0000-0002-7356-1779
created: 2024-03-18

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
sub property of: alternative label

has narrow synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
sub property of: alternative label

has related synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
sub property of: alternative label

label
type: AnnotationProperty
editor preferred term: label

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative label: part_of
RO_0001900: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative label: has_part
imported from: iao.owl
RO_0001900: RO_0001901

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
type: ObjectProperty
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: preceded by
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative label: is preceded by
alternative label: preceded_by
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: precedes

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred term: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative label: occurs_in
alternative label: unfolds in
alternative label: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred term: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
editor preferred term: has measurement unit label
imported from: iao.owl

is about
type: ObjectProperty
editor preferred term: is about
definition: A (currently) primitive relation that relates an information artifact to an entity.
imported from: iao.owl

denotes
type: ObjectProperty
sub property of: is about
editor preferred term: denotes
definition: A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
imported from: iao.owl

is quality measurement of
type: ObjectProperty
sub property of: is about
editor preferred term: is quality measurement of
definition: m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
imported from: iao.owl

denoted by
type: ObjectProperty
editor preferred term: denoted by
definition: inverse of the relation 'denotes'
imported from: iao.owl

has coordinate unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
editor preferred term: has coordinate unit label
imported from: iao.owl

is duration of
type: ObjectProperty
sub property of: is about
editor preferred term: is duration of
definition: relates a process to a time-measurement-datum that represents the duration of the process
imported from: iao.owl

provides_service_consumer_with
type: ObjectProperty
sub property of: has part
domain: service
editor preferred term: provides_service_consumer_with
example of usage: 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.
has curation status: IAO_0000123
definition: A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.

is_supported_by_data
type: ObjectProperty
domain: OBI_0001909
range: data item
editor preferred term: is_supported_by_data
example of usage: 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.
has curation status: IAO_0000122
definition: 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
term editor: OBI
definition source: OBI
definition source: Philly 2011 workshop

has specified input
type: ObjectProperty
sub property of: has participant
inverse of: is specified input of
domain: planned process
editor preferred term: has specified input
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
definition: The inverse property of is specified input of
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot

obsolete_is_concretization_of
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: is_concretization_of
has curation status: IAO_0000123
definition: 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.
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000058
term editor: PERSON: Alan Ruttenburg
term editor: PERSON: Barry Smith
has obsolescence reason: IAO_0000228
deprecated: true

is specified input of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is specified input of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters

obsolete_is_concretized_as
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: is_concretized_as
has curation status: IAO_0000123
definition: 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.
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000059
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
has obsolescence reason: IAO_0000228
deprecated: true

obsolete_has_quality
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: has_quality
has curation status: IAO_0000122
definition: 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]
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000086
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
has obsolescence reason: IAO_0000228
deprecated: true

has specified output
type: ObjectProperty
sub property of: has participant
inverse of: is specified output of
domain: planned process
editor preferred term: has specified output
has curation status: IAO_0000122
definition: The inverse property of is specified output of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot

obsolete_is_realized_by
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: is_realized_by
has curation status: IAO_0000122
definition: Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
editor note: replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
alternative label: executed_during
alternative label: has_realization
alternative label: is_realized_as
has obsolescence reason: IAO_0000228
deprecated: true

obsoleted_has_specified_output_information
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsoleted_has_specified_output_information
has curation status: IAO_0000123
definition: A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Frank Gibson
has obsolescence reason: IAO_0000103
deprecated: true

is_manufactured_by
type: ObjectProperty
domain: material entity
range: manufacturer
editor preferred term: is_manufactured_by
example of usage: http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
has curation status: IAO_0000123
definition: c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
term editor: Alan Ruttenberg
term editor: Liju Fan
alternative label: has_make
alternative label: has_manufacturer

obsolete_has_function
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: has_function
example of usage: heart has_function to-pump-blood
has curation status: IAO_0000122
definition: Relation between an independent continuant and a function.
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000085
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
has obsolescence reason: IAO_0000228
deprecated: true

obsoleted_is_reagent_in
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsoleted_is_reagent_in
example of usage: some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: IAO_0000123
definition: Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
term editor: Alan Ruttenberg
has obsolescence reason: IAO_0000103
deprecated: true

obsolete_realizes
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: realizes
example of usage: example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes.
has curation status: IAO_0000122
definition: Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
editor note: replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungal
alternative label: executes
alternative label: has_function_part
alternative label: involves_execution_of
alternative label: is_realization_of
has obsolescence reason: IAO_0000228
deprecated: true

obsoleted_utilizes_reagent
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsoleted_utilizes_reagent
example of usage: see example_of_usage for is_reagent_in
has curation status: IAO_0000123
definition: Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
term editor: Alan Ruttenberg
has obsolescence reason: IAO_0000103
deprecated: true

obsoleted_is_device_for
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsoleted_is_device_for
example of usage: some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: IAO_0000123
definition: Relationship between a device and a protocol application in which it participates
term editor: Alan Ruttenberg
has obsolescence reason: IAO_0000103
deprecated: true

is specified output of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred term: is specified output of
has curation status: IAO_0000122
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters

obsoleted_utilizes_device
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsoleted_utilizes_device
example of usage: see example_of_usage for is_device_for
has curation status: IAO_0000123
definition: Relationship between protocol application and an intrument in which it participates
term editor: Alan Ruttenberg
has obsolescence reason: IAO_0000103
deprecated: true

is_proxy_for
type: ObjectProperty
editor preferred term: is_proxy_for
example of usage: position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity
has curation status: IAO_0000123
definition: A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
editor note: A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition)
term editor: Alan Ruttenberg

obsoleted_has_specified_input_information
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: has specified input information
has curation status: IAO_0000123
definition: A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
term editor: PERSON: Frank Gibson
term editor: PERSON:Alan Ruttenberg
alternative label: consumes data
has obsolescence reason: IAO_0000103
deprecated: true

obsolete_has_role
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: has_role
has curation status: IAO_0000122
definition: A relation between a continuant C and a role R. The reciprocal relation of role_of.
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000087
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON:Chris Mungal
has obsolescence reason: IAO_0000228
deprecated: true

obsolete_results_from
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsolete_results_from
has curation status: IAO_0000123
editor note: 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the
has obsolescence reason: IAO_0000103
deprecated: true

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred term: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: IAO_0000120
definition: 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.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

obsoleted_is_specified_information_output_of
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: is_specified_information_output_of
has curation status: IAO_0000120
definition: A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
editor note: is replaced by has_specified_output_of
term editor: PERSON: James Malone
definition source: Editor
has obsolescence reason: IAO_0000103
deprecated: true

has grain
type: ObjectProperty
sub property of: has part
editor preferred term: has grain
has curation status: IAO_0000120
definition: 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.
editor note: 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
term editor: PERSON: Alan Ruttenberg
definition source: 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

obsoleted_is_specified_information_intput_of
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: obsoleted_is_specified_information_intput_of
has curation status: IAO_0000123
definition: Is the inverse relation of has_specfied_input_information
editor note: is replaced by is_specified_intput_of
has obsolescence reason: IAO_0000103
deprecated: true

is grain of
type: ObjectProperty
sub property of: part of
editor preferred term: is grain of
has curation status: IAO_0000120
definition: 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.
editor note: JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic.
term editor: PERSON: Alan Ruttenberg
definition source: 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

provisions
type: ObjectProperty
inverse of: has_supplier
editor preferred term: provisions
has curation status: IAO_0000123
definition: 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
editor note: 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.
term editor: GROUP: Relations branch
alternative label: supplies

has_supplier
type: ObjectProperty
domain: material entity
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred term: has_supplier
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Alan Rutternberg
term editor: PERSON: Cristian Cocos
term editor: PERSON: Frank Gibson
term editor: PERSON: Melanie Courtot

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred term: objective_achieved_by
has curation status: IAO_0000122
definition: 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.
term editor: OBI
definition source: OBI

is member of organization
type: ObjectProperty
inverse of: has organization member
domain: Class
  union of: Homo sapiens
  union of: organization
range: organization
editor preferred term: is member of organization
has curation status: IAO_0000120
definition: 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.
editor note: 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
editor note: 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.
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

has category label
type: ObjectProperty
sub property of: has part
domain: categorical measurement datum
range: categorical label
editor preferred term: has category label
has curation status: IAO_0000123
definition: 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 disposition to bind
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
editor preferred term: has disposition to bind
has curation status: IAO_0000123
definition: A relationship between two material entitites that each have disposition to form a complex with the other.
editor note: 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
definition source: IEDB

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred term: has organization member
has curation status: IAO_0000123
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
term editor: Person: Jie Zheng

specifies value of
type: ObjectProperty
sub property of: is about
domain: OBI_0001933
editor preferred term: specifies value of
has curation status: IAO_0000123
definition: A relation between a value specification and an entity which the specification is about.

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: OBI_0001933
editor preferred term: has value specification
has curation status: IAO_0000120
definition: A relation between an information content entity and a value specification that specifies its value.
term editor: PERSON: James A. Overton
definition source: OBI

has performer
type: ObjectProperty
sub property of: has participant
domain: planned process
range: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
    union of: device
  intersection of: Restriction
    on property: has role
    some values from: investigation agent role
editor preferred term: has performer
has curation status: IAO_0000428
definition: 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.
term editor: OBI
definition source: OBI
comment: 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).

has assay target context
type: ObjectProperty
range: material entity
editor preferred term: has assay target context
has curation status: IAO_0000120
definition: 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.
term editor: Hector Guzman-Orozco
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1516

has study design
type: ObjectProperty
inverse of: is study design of
domain: investigation
range: OBI_0500000
editor preferred term: has study design
has curation status: IAO_0000123
definition: A relation between an investigation and a study design in which part of the investigation is a study design execution that carries out the study design.
term editor: Sebastian Duesing
term tracker item: https://github.com/obi-ontology/obi/issues/1831
ontology term requester: Charlie Hoyt

is study design of
type: ObjectProperty
domain: OBI_0500000
range: investigation
editor preferred term: is study design of
has curation status: IAO_0000123
definition: A relation between a study design and an investigation when part of the investigation is a study design execution that carries out the study design.
term editor: Sebastian Duesing
term tracker item: https://github.com/obi-ontology/obi/issues/1831
ontology term requester: Charlie Hoyt

process is result of
type: ObjectProperty
sub property of: immediately preceded by
editor preferred term: process is result of
example of usage: The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
has curation status: IAO_0000123
definition: is a relationship between a process and a preceding occurrent that directly caused the later one to occur
term editor: IEDB
term editor: PERSON:Bjoern Peters

obsolete_is_described_by
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred term: is_described_by
has curation status: IAO_0000123
has obsolescence reason: IAO_0000103
deprecated: true

bound_to
type: ObjectProperty
domain: material entity
range: material entity
editor preferred term: bound_to
has curation status: IAO_0000123
definition: A relationship between two material entities that form a complex based on a selective, non-covalent interaction.
editor note: 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.

characteristic of
type: ObjectProperty
inverse of: has characteristic
type: FunctionalProperty
editor preferred term: inheres in
example of usage: this fragility is a characteristic of this vase
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
alternative label: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative label: function_of
alternative label: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative label: is role of
alternative label: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative label: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative label: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

derives from
type: ObjectProperty
sub property of: topObjectProperty
inverse of: derives into
editor preferred term: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: IAO_0000125
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative label: derives_from
imported from: ro.owl

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: IAO_0000125
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative label: derives_into

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred term: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative label: location_of
RO_0001900: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred term: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative label: located_in
RO_0001900: RO_0001901
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: 2D_boundary_of
alternative label: boundary of
alternative label: is 2D boundary of
alternative label: is boundary of
RO_0001900: RO_0001901

has 2D boundary
type: ObjectProperty
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: has boundary
alternative label: has_2D_boundary
RO_0001900: RO_0001901

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
term editor: David Osumi-Sutherland
alternative label: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: David Osumi-Sutherland
alternative label: ends_at_start_of
alternative label: meets
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

has component
type: ObjectProperty
sub property of: has part
has curation status: IAO_0000125
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901

capable of
type: ObjectProperty
domain: independent continuant
range: process
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
alternative label: has function realized in

surrounded by
type: ObjectProperty
sub property of: adjacent to
editor preferred term: surrounded by
definition: x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
imported from: ro.owl

adjacent to
type: ObjectProperty

temporal relation
type: ObjectProperty
range: occurrent
has curation status: IAO_0000125
editor note: move to BFO?
definition source: Allen
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporal relation
has curation status: IAO_0000125
definition: inverse of starts with
term editor: Chris Mungall
definition source: Allen

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

DEPRECATED inheres in
type: ObjectProperty
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
deprecated: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

has measurement value
type: DatatypeProperty
type: FunctionalProperty
editor preferred term: has measurement value
imported from: iao.owl

has_feature_value
type: DatatypeProperty
domain: OBI_0200140
editor preferred term: has_feature_value
has curation status: IAO_0000123
definition: has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.
term editor: James Malone

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: OBI_0001933
range: real
editor preferred term: has specified numeric value
has curation status: IAO_0000120
definition: A relation between a value specification and a number that quantifies it.
editor note: 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.
term editor: PERSON: James A. Overton
definition source: OBI

has specified value
type: DatatypeProperty
domain: OBI_0001933
editor preferred term: has specified value
has curation status: IAO_0000123
definition: A relation between a value specification and a literal.
editor note: 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.
definition source: OBI

has representation
type: DatatypeProperty
editor preferred term: has representation
example of usage: 12th arrondissement of Paris
example of usage: 20g
example of usage: I feel sick to my stomach every Tuesday
has curation status: IAO_0000122
definition: 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text.
editor note: Further processing may enable the value to be represented in a component data structure such as an OBI value specification.
term editor: Damion Dooley
term editor: Mark Miller
date: 2019-07-14T07:05:50Z

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: pato.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object
BFO CLIF specification label: FiatObjectPart
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]

Axiom
annotated source: fiat object
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
editor preferred term: material entity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: ido.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative label: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: elucidation
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

insulin
type: Class
subclass of: peptide
editor preferred term: insulin
definition: A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies.
imported from: chebi.owl

water
type: Class
subclass of: molecular entity
editor preferred term: water
definition: An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms
imported from: chebi.owl

ATP
type: Class
subclass of: molecular entity
editor preferred term: ATP
definition: An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways.
imported from: chebi.owl

biotin
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: biotin
definition: An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
imported from: chebi.owl

cholesterol
type: Class
subclass of: molecular entity
editor preferred term: cholesterol
definition: A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.
imported from: chebi.owl

ammonia
type: Class
subclass of: molecular entity
editor preferred term: ammonia
definition: An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
imported from: chebi.owl

phospholipid
type: Class
subclass of: molecular entity
editor preferred term: phospholipid
definition: A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides.
imported from: chebi.owl

nitrite
type: Class
subclass of: molecular entity
editor preferred term: nitrite
definition: The nitrogen oxoanion formed by loss of a proton from nitrous acid.
imported from: chebi.owl

carbon dioxide
type: Class
subclass of: molecular entity
editor preferred term: carbon dioxide
definition: A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food.
imported from: chebi.owl

peptide
type: Class
subclass of: macromolecule
editor preferred term: peptide
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl

globulin type
type: Class
subclass of: macromolecule
editor preferred term: globulin type
definition: One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma.
imported from: chebi.owl

creatinine
type: Class
subclass of: molecular entity
editor preferred term: creatinine
definition: A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
imported from: chebi.owl

mycophenolic acid
type: Class
subclass of: molecular entity
editor preferred term: mycophenolic acid
definition: A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases.
imported from: chebi.owl

creatine
type: Class
subclass of: molecular entity
editor preferred term: creatine
definition: A glycine derivative having methyl and amidino groups attached to the nitrogen.
imported from: chebi.owl

bilirubin IXalpha
type: Class
subclass of: molecular entity
editor preferred term: bilirubin IXalpha
definition: A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
imported from: chebi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred term: deoxyribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl

progesterone
type: Class
subclass of: molecular entity
editor preferred term: progesterone
definition: A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species.
imported from: chebi.owl

hydrogensulfite
type: Class
subclass of: molecular entity
editor preferred term: hydrogensulfite
imported from: chebi.owl

homocysteine
type: Class
subclass of: amino acid
editor preferred term: homocysteine
definition: A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain.
imported from: chebi.owl

glucose
type: Class
subclass of: molecular entity
editor preferred term: glucose
definition: An aldohexose used as a source of energy and metabolic intermediate.
imported from: chebi.owl

testosterone
type: Class
subclass of: molecular entity
editor preferred term: testosterone
definition: An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5..
imported from: chebi.owl

methemoglobin
type: Class
subclass of: macromolecule
editor preferred term: methemoglobin
definition: A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin.
imported from: chebi.owl

hydrogencarbonate
type: Class
subclass of: molecular entity
editor preferred term: hydrogencarbonate
definition: The carbon oxoanion resulting from the removal of a proton from carbonic acid.
imported from: chebi.owl

cortisol
type: Class
subclass of: molecular entity
editor preferred term: cortisol
definition: A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses.
imported from: chebi.owl

5'-adenylyl sulfate
type: Class
subclass of: molecular entity
editor preferred term: 5'-adenylyl sulfate
definition: An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups.
imported from: chebi.owl

triglyceride
type: Class
subclass of: molecular entity
editor preferred term: triglyceride
definition: Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids.
imported from: chebi.owl

chloride
type: Class
subclass of: molecular entity
editor preferred term: chloride
definition: A halide anion formed when chlorine picks up an electron to form an an anion.
imported from: chebi.owl

3-hydroxybutyric acid
type: Class
subclass of: fatty acid
editor preferred term: 3-hydroxybutyric acid
definition: A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics.
imported from: chebi.owl

bile salt
type: Class
subclass of: molecular entity
editor preferred term: bile salt
definition: A sodium salt of the conjugate of any bile acid with either glycine or taurine.
imported from: chebi.owl

molecular entity
type: Class
subclass of: material entity
editor preferred term: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl

cytochalasin
type: Class
subclass of: molecular entity
editor preferred term: cytochalasin
imported from: chebi.owl

estradiol
type: Class
subclass of: molecular entity
editor preferred term: estradiol
definition: A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17.
imported from: chebi.owl

N-ethyl-N-nitrosourea
type: Class
subclass of: molecular entity
editor preferred term: N-ethyl-N-nitrosourea
definition: A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups.
imported from: chebi.owl

proton
type: Class
subclass of: molecular entity
editor preferred term: proton
definition: Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
imported from: chebi.owl

iron cation
type: Class
subclass of: molecular entity
editor preferred term: iron cation
imported from: chebi.owl

luciferin
type: Class
subclass of: molecular entity
editor preferred term: luciferin
definition: A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
imported from: chebi.owl

amikacin
type: Class
subclass of: molecular entity
editor preferred term: amikacin
definition: An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group.
imported from: chebi.owl

sodium chloride
type: Class
subclass of: molecular entity
editor preferred term: sodium chloride
definition: An inorganic chloride salt having sodium(1+) as the counterion.
imported from: chebi.owl

uric acid
type: Class
subclass of: molecular entity
editor preferred term: uric acid
definition: An oxopurine that is the final oxidation product of purine metabolism.
imported from: chebi.owl

lead(0)
type: Class
subclass of: molecular entity
editor preferred term: lead(0)
imported from: chebi.owl

vancomycin
type: Class
subclass of: peptide
editor preferred term: vancomycin
definition: A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile.
imported from: chebi.owl

rac-lactic acid
type: Class
subclass of: material entity
editor preferred term: rac-lactic acid
definition: A racemate comprising equimolar amounts of (R)- and (S)-lactic acid.
imported from: chebi.owl

acrylamide
type: Class
subclass of: molecular entity
editor preferred term: acrylamide
definition: A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
imported from: chebi.owl

dehydroepiandrosterone
type: Class
subclass of: molecular entity
editor preferred term: dehydroepiandrosterone
definition: An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands.
imported from: chebi.owl

3,3',5'-triiodothyronine
type: Class
subclass of: amino acid
editor preferred term: 3,3',5'-triiodothyronine
imported from: chebi.owl

tobramycin
type: Class
subclass of: molecular entity
editor preferred term: tobramycin
definition: A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring.
imported from: chebi.owl

sodium(1+)
type: Class
subclass of: molecular entity
editor preferred term: sodium(1+)
definition: A monoatomic monocation obtained from sodium.
imported from: chebi.owl

potassium(1+)
type: Class
subclass of: molecular entity
editor preferred term: potassium(1+)
definition: A monoatomic monocation obtained from potassium.
imported from: chebi.owl

hydroxyl
type: Class
subclass of: molecular entity
editor preferred term: hydroxyl
imported from: chebi.owl

deuterium atom
type: Class
subclass of: molecular entity
subclass of: atom
editor preferred term: deuterium atom
definition: The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).
imported from: chebi.owl

thyroxine
type: Class
subclass of: amino acid
editor preferred term: thyroxine
definition: An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions.
imported from: chebi.owl

ruthenium atom
type: Class
subclass of: molecular entity
editor preferred term: ruthenium atom
imported from: chebi.owl

fluorescein (lactone form)
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: fluorescein (lactone form)
definition: A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy.
imported from: chebi.owl

gadodiamide hydrate
type: Class
subclass of: molecular entity
editor preferred term: gadodiamide hydrate
definition: The hydrate of gadodiamide.
imported from: chebi.owl

gadoteridol
type: Class
subclass of: molecular entity
editor preferred term: gadoteridol
definition: A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
imported from: chebi.owl

phenol red
type: Class
subclass of: molecular entity
editor preferred term: phenol red
definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney.
imported from: chebi.owl

sodium citrate dihydrate
type: Class
subclass of: molecular entity
editor preferred term: sodium citrate dihydrate
definition: The dihydrate of trisodium citrate.
imported from: chebi.owl

methyl group
type: Class
subclass of: molecular entity
editor preferred term: methyl group
definition: An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom.
imported from: chebi.owl

atom
type: Class
subclass of: material entity
editor preferred term: atom
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl

elemental oxygen
type: Class
subclass of: molecular entity
editor preferred term: elemental oxygen
imported from: chebi.owl

rare earth metal atom
type: Class
subclass of: atom
editor preferred term: rare earth metal atom
imported from: chebi.owl

rhodium atom
type: Class
subclass of: molecular entity
editor preferred term: rhodium atom
definition: A cobalt group element atom of atomic number 45.
imported from: chebi.owl

gadolinium atom
type: Class
subclass of: molecular entity
editor preferred term: gadolinium atom
imported from: chebi.owl

terbium atom
type: Class
subclass of: molecular entity
editor preferred term: terbium atom
imported from: chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
editor preferred term: nucleic acid
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred term: ribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl

amino acid
type: Class
subclass of: molecular entity
editor preferred term: amino acid
definition: A carboxylic acid containing one or more amino groups.
imported from: chebi.owl

macromolecule
type: Class
subclass of: molecular entity
editor preferred term: macromolecule
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative label: polymer
imported from: chebi.owl

hemoglobin
type: Class
subclass of: macromolecule
editor preferred term: hemoglobin
imported from: chebi.owl

fatty acid
type: Class
subclass of: molecular entity
editor preferred term: fatty acid
definition: Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids.
imported from: chebi.owl

gadolinium molecular entity
type: Class
subclass of: molecular entity
editor preferred term: gadolinium molecular entity
imported from: chebi.owl

phosphate ion
type: Class
subclass of: molecular entity
editor preferred term: phosphate ion
definition: A phosphorus oxoanion that is the conjugate base of phosphoric acid.
imported from: chebi.owl

gadodiamide
type: Class
subclass of: molecular entity
editor preferred term: gadodiamide
definition: A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
imported from: chebi.owl

folic acids
type: Class
subclass of: molecular entity
editor preferred term: folic acids
definition: A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units.
imported from: chebi.owl

sodium phosphate
type: Class
subclass of: molecular entity
editor preferred term: sodium phosphate
imported from: chebi.owl

phosphorus-32 atom
type: Class
subclass of: atom
subclass of: OBI_0001879
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: phosphorus-32 atom
definition: The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
imported from: chebi.owl

phosphorus-33 atom
type: Class
subclass of: atom
subclass of: OBI_0001879
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: phosphorus-33 atom
definition: The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
imported from: chebi.owl

Cy3 dye
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: Cy3 dye
imported from: chebi.owl

Cy5 dye
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: Cy5 dye
imported from: chebi.owl

high-density lipoprotein
type: Class
subclass of: lipoprotein
editor preferred term: high-density lipoprotein
definition: A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. They are synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport).
imported from: chebi.owl

low-density lipoprotein
type: Class
subclass of: lipoprotein
editor preferred term: low-density lipoprotein
definition: A class of lipoproteins of small size (18-25 nm) and low density (1.019-1.063 g/ml) particles with a core composed mainly of cholesterol esters and smaller amounts of triglycerides. The surface monolayer consists mostly of phospholipids, a single copy of apolipoprotein B-100, and free cholesterol molecules. The main function of LDL is to transport cholesterol and cholesterol esters from the liver. Excessive levels are associated with cardiovascular disease.
imported from: chebi.owl

very-low-density lipoprotein
type: Class
subclass of: lipoprotein
editor preferred term: very-low-density lipoprotein
definition: A class of lipoproteins of large size (30-80 nm), very low density (0.93-1.006 g/ml) particles with a core composed mainly of triglycerides and a surface monolayer of phospholipids and cholesterol into which are imbedded the apolipoproteins B, E, and C. VLDL facilitate the transport of endogenously made triglycerides to extrahepatic tissues.
imported from: chebi.owl

calcium cation
type: Class
subclass of: calcium ion
editor preferred term: calcium cation
imported from: chebi.owl

calcium ion
type: Class
subclass of: molecular entity
editor preferred term: calcium ion
imported from: chebi.owl

magnesium cation
type: Class
subclass of: molecular entity
editor preferred term: magnesium cation
definition: Any magnesium ion that is positively charged.
imported from: chebi.owl

valproic acid
type: Class
subclass of: fatty acid
editor preferred term: valproic acid
definition: A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem.
imported from: chebi.owl

digoxigenin
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: digoxigenin
definition: A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis.
imported from: chebi.owl

EDTA(4-)
type: Class
subclass of: molecular entity
editor preferred term: EDTA(4-)
definition: A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA).
imported from: chebi.owl

deoxyribonucleotide
type: Class
subclass of: molecular entity
editor preferred term: deoxyribonucleotide
definition: A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen.
imported from: chebi.owl

digoxin
type: Class
subclass of: molecular entity
editor preferred term: digoxin
definition: A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small.
imported from: chebi.owl

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
editor preferred term: double-stranded DNA
imported from: chebi.owl

5-bromo-2'-deoxyuridine
type: Class
subclass of: molecular entity
editor preferred term: 5-bromo-2'-deoxyuridine
definition: A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
imported from: chebi.owl

low-density lipoprotein cholesterol
type: Class
subclass of: molecular entity
editor preferred term: low-density lipoprotein cholesterol
definition: Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL).
imported from: chebi.owl

high-density lipoprotein cholesterol
type: Class
subclass of: molecular entity
editor preferred term: high-density lipoprotein cholesterol
definition: Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL).
imported from: chebi.owl

chromium-51
type: Class
subclass of: molecular entity
editor preferred term: chromium-51
definition: A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
imported from: chebi.owl

Alexa Fluor 532
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: Alexa Fluor 532
imported from: chebi.owl

Alexa Fluor 546
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: Alexa Fluor 546
imported from: chebi.owl

Alexa Fluor 555
type: Class
subclass of: OBI_0002744
subclass of: Restriction
  on property: has role
  some values from: OBI_0002743
editor preferred term: Alexa Fluor 555
definition: A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
imported from: chebi.owl

tritiated thymidine
type: Class
subclass of: molecular entity
editor preferred term: tritiated thymidine
definition: Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
imported from: chebi.owl

dimethyl sulfate
type: Class
subclass of: molecular entity
editor preferred term: dimethyl sulfate
definition: The dimethyl ester of sulfuric acid.
imported from: chebi.owl

diethyl pyrocarbonate
type: Class
subclass of: molecular entity
editor preferred term: diethyl pyrocarbonate
definition: The diethyl ester of dicarbonic acid.
imported from: chebi.owl

1,1-dihydroxy-3-ethoxy-2-butanone
type: Class
subclass of: molecular entity
editor preferred term: 1,1-dihydroxy-3-ethoxy-2-butanone
definition: A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
imported from: chebi.owl

N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
type: Class
subclass of: molecular entity
editor preferred term: N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
definition: A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
imported from: chebi.owl

N-methylisatoic anhydride
type: Class
subclass of: molecular entity
editor preferred term: N-methylisatoic anhydride
definition: A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
imported from: chebi.owl

(S)-1-(4-bromoacetamidobenzyl)EDTA
type: Class
subclass of: molecular entity
editor preferred term: (S)-1-(4-bromoacetamidobenzyl)EDTA
definition: A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
imported from: chebi.owl

EDTA methidiumpropylamide
type: Class
subclass of: molecular entity
editor preferred term: EDTA methidiumpropylamide
definition: A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
imported from: chebi.owl

bromophenol blue
type: Class
subclass of: molecular entity
editor preferred term: bromophenol blue
definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
imported from: chebi.owl

tacrolimus hydrate
type: Class
subclass of: molecular entity
editor preferred term: tacrolimus hydrate
definition: A hydrate that is the monohydrate form of tacrolimus.
imported from: chebi.owl

oxygen radical
type: Class
subclass of: molecular entity
editor preferred term: oxygen radical
definition: An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species.
imported from: chebi.owl

lipoprotein
type: Class
subclass of: macromolecule
editor preferred term: lipoprotein
definition: A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids.
imported from: chebi.owl

thyroid stimulating hormone
type: Class
subclass of: macromolecule
editor preferred term: thyroid stimulating hormone
imported from: chebi.owl

Luteinizing hormone
type: Class
subclass of: molecular entity
editor preferred term: Luteinizing hormone
imported from: chebi.owl

Follicle stimulating hormone
type: Class
subclass of: molecular entity
editor preferred term: Follicle stimulating hormone
imported from: chebi.owl

25-hydroxyvitamin D2
type: Class
subclass of: molecular entity
editor preferred term: 25-hydroxyvitamin D2
definition: A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group.
imported from: chebi.owl

tris
type: Class
subclass of: molecular entity
editor preferred term: tris
definition: A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
imported from: chebi.owl

fluorescence microscopy assay
type: Class
subclass of: light microscopy assay
subclass of: fluorescence detection assay
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has characteristic
      some values from: PATO_0000018
definition: Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
alternative label: FM
alternative label: fluorescence imaging
alternative label: fluorescence microscopic imaging
definition source: CHMO

confocal fluorescence microscopy assay
type: Class
subclass of: OBI_0002119
definition: Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence.
alternative label: CLSM
alternative label: LSCM
alternative label: confocal fluorescence imaging
alternative label: confocal laser scanning fluorescence microscopy
alternative label: confocal laser scanning microscopy
alternative label: confocal-laser scanning microscopy
alternative label: fluorescence confocal microscopy
alternative label: fluorescence confocal scanning laser microscopy
alternative label: scanning confocal fluorescence microscopy
definition source: CHMO

light microscopy assay
type: Class
subclass of: OBI_0002119
definition: Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
alternative label: OM
alternative label: light microscopy
alternative label: optical microscopy
definition source: CHMO

liquid chromatography-tandem mass spectrometry
type: Class
subclass of: OBI_0003097
subclass of: OBI_0003540
subclass of: Restriction
  on property: has part
  some values from: OBI_0003547
definition: A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series.
alternative label: LC-MS-MS
alternative label: LC-MS/MS
alternative label: LC-MS2
alternative label: LC-MSMS
alternative label: LC/MS/MS
alternative label: LCMSMS
alternative label: liquid chromatography tandem mass spectrometry
alternative label: liquid chromatography tandem mass spectroscopy
alternative label: liquid chromatography-tandem mass spectroscopy
definition source: CHMO

cell line cell
type: Class
subclass of: OBI_0001866
subclass of: Class
  union of: Restriction
    on property: is specified output of
    some values from: OBI_0001867
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is specified output of
      some values from: OBI_0001867
subclass of: Restriction
editor preferred term: cell line cell
definition: A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
imported from: clo.owl

Axiom
annotated source: cell line cell
annotated property: subClassOf
annotated target: Restriction
editor note: 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time.

mortal cell line cell
type: Class
subclass of: cell line cell
editor preferred term: mortal cell line cell
definition: A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence.
imported from: clo.owl

immortal cell line cell
type: Class
subclass of: cell line cell
editor preferred term: immortal cell line cell
definition: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
imported from: clo.owl

cell line
type: Class
subclass of: OBI_0001905
subclass of: Restriction
  on property: has grain
  some values from: cell line cell
subclass of: Restriction
  on property: has grain
  all values from: cell line cell
editor preferred term: cell line
definition: A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
imported from: clo.owl

immortal cell line
type: Class
subclass of: cell line
subclass of: Restriction
  on property: has grain
  some values from: immortal cell line cell
subclass of: Restriction
  on property: has grain
  all values from: immortal cell line cell
editor preferred term: immortal cell line
definition: A cell line that is expected to be capable of indefinite propagation in an vitro culture.
imported from: clo.owl

mortal cell line
type: Class
subclass of: cell line
subclass of: Restriction
  on property: has grain
  some values from: mortal cell line cell
subclass of: Restriction
  on property: has grain
  all values from: mortal cell line cell
subclass of: Restriction
  on property: is specified output of
  qualified cardinality: 0
  on class: cell line immortalization
editor preferred term: mortal cell line
definition: A cell line is able to support only a limited number of passages in vitro.
imported from: clo.owl

cell
type: Class
subclass of: material entity
editor preferred term: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl

primary cultured cell
type: Class
subclass of: cultured cell
subclass of: Class
  complement of: Restriction
    on property: is specified output of
    some values from: OBI_0600037
subclass of: Class
  complement of: Restriction
    on property: derives from
    some values from: Class
      intersection of: cultured cell
      intersection of: Restriction
        on property: is specified output of
        some values from: OBI_0600037
editor preferred term: primary cultured cell
definition: A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
imported from: cl.owl

obsolete native cell
type: Class
subclass of: cell
editor preferred term: obsolete native cell
definition: OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
imported from: cl.owl

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is specified output of
    some values from: OBI_0600036
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is specified output of
      some values from: OBI_0600036
editor preferred term: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl

sperm
type: Class
subclass of: cell
editor preferred term: sperm
definition: A mature male germ cell that develops from a spermatid.
imported from: cl.owl

fibroblast
type: Class
subclass of: cell
editor preferred term: fibroblast
definition: A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
imported from: cl.owl

epithelial cell
type: Class
subclass of: cell
editor preferred term: epithelial cell
definition: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
imported from: cl.owl

mesothelial cell
type: Class
subclass of: epithelial cell
editor preferred term: mesothelial cell
definition: A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.
imported from: cl.owl

T cell
type: Class
subclass of: lymphocyte
editor preferred term: T cell
definition: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
imported from: cl.owl

mast cell
type: Class
subclass of: cell
editor preferred term: mast cell
definition: A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
imported from: cl.owl

hepatocyte
type: Class
subclass of: epithelial cell
editor preferred term: hepatocyte
definition: The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
imported from: cl.owl

erythrocyte
type: Class
subclass of: cell
editor preferred term: erythrocyte
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
imported from: cl.owl

platelet
type: Class
subclass of: cell
editor preferred term: platelet
definition: A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
imported from: cl.owl

macrophage
type: Class
subclass of: cell
editor preferred term: macrophage
definition: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
imported from: cl.owl

B cell
type: Class
subclass of: lymphocyte
editor preferred term: B cell
definition: A lymphocyte of B lineage that is capable of B cell mediated immunity.
imported from: cl.owl

dendritic cell
type: Class
subclass of: cell
editor preferred term: dendritic cell
definition: A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
imported from: cl.owl

neuron
type: Class
subclass of: neural cell
editor preferred term: neuron
definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
imported from: cl.owl

lymphocyte
type: Class
subclass of: mononuclear cell
editor preferred term: lymphocyte
definition: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
imported from: cl.owl

megakaryocyte
type: Class
subclass of: cell
editor preferred term: megakaryocyte
definition: A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
imported from: cl.owl

reticulocyte
type: Class
subclass of: cell
editor preferred term: reticulocyte
definition: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
imported from: cl.owl

band form neutrophil
type: Class
subclass of: neutrophil
editor preferred term: band form neutrophil
definition: A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative.
imported from: cl.owl

nucleate erythrocyte
type: Class
subclass of: erythrocyte
editor preferred term: nucleate erythrocyte
definition: An erythrocyte having a nucleus.
imported from: cl.owl

monocyte
type: Class
subclass of: leukocyte
subclass of: mononuclear cell
editor preferred term: monocyte
definition: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
imported from: cl.owl

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: material processing
editor preferred term: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl

natural killer cell
type: Class
subclass of: lymphocyte
editor preferred term: natural killer cell
definition: A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
imported from: cl.owl

CD4-positive, alpha-beta T cell
type: Class
subclass of: alpha-beta T cell
editor preferred term: CD4-positive, alpha-beta T cell
definition: A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
imported from: cl.owl

CD8-positive, alpha-beta T cell
type: Class
subclass of: alpha-beta T cell
editor preferred term: CD8-positive, alpha-beta T cell
definition: A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
imported from: cl.owl

leukocyte
type: Class
subclass of: cell
editor preferred term: leukocyte
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
imported from: cl.owl

basophil
type: Class
subclass of: cell
editor preferred term: basophil
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
imported from: cl.owl

eosinophil
type: Class
subclass of: leukocyte
editor preferred term: eosinophil
definition: Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive.
imported from: cl.owl

neutrophil
type: Class
subclass of: leukocyte
editor preferred term: neutrophil
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
imported from: cl.owl

immature neutrophil
type: Class
subclass of: neutrophil
editor preferred term: immature neutrophil
definition: Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking.
imported from: cl.owl

plasma cell
type: Class
subclass of: B cell
editor preferred term: plasma cell
definition: A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
imported from: cl.owl

alpha-beta T cell
type: Class
subclass of: T cell
editor preferred term: alpha-beta T cell
definition: A T cell that expresses an alpha-beta T cell receptor complex.
imported from: cl.owl

CD8-positive, alpha-beta cytotoxic T cell
type: Class
subclass of: CD8-positive, alpha-beta T cell
editor preferred term: CD8-positive, alpha-beta cytotoxic T cell
definition: A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
imported from: cl.owl

mature NK T cell
type: Class
subclass of: alpha-beta T cell
editor preferred term: mature NK T cell
definition: A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
imported from: cl.owl

promyelocyte
type: Class
subclass of: cell
editor preferred term: promyelocyte
definition: A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative.
imported from: cl.owl

mononuclear cell
type: Class
subclass of: cell
editor preferred term: mononuclear cell
definition: A leukocyte with a single non-segmented nucleus in the mature form.
imported from: cl.owl

malignant cell
type: Class
subclass of: cell
editor preferred term: malignant cell
definition: A neoplastic cell that is capable of entering a surrounding tissue
imported from: cl.owl

metamyelocyte
type: Class
subclass of: cell
editor preferred term: metamyelocyte
definition: A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare.
imported from: cl.owl

myelocyte
type: Class
subclass of: cell
editor preferred term: myelocyte
definition: A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses.
imported from: cl.owl

neural cell
type: Class
subclass of: cell
editor preferred term: neural cell
definition: A cell that is part of the nervous system.
imported from: cl.owl

segmented neutrophil of bone marrow
type: Class
subclass of: neutrophil
editor preferred term: segmented neutrophil of bone marrow
definition: A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface.
imported from: cl.owl

peripheral blood mononuclear cell
type: Class
subclass of: mononuclear cell
editor preferred term: peripheral blood mononuclear cell
definition: A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.
imported from: cl.owl

complex of molecules
type: Class
subclass of: material entity
editor preferred term: complex of molecules
definition: A complex of two or more molecular entities that are not covalently bound.
imported from: cob.owl

soil
type: Class
subclass of: material entity
editor preferred term: soil
definition: An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms.
imported from: envo.owl

podzol
type: Class
subclass of: soil
editor preferred term: podzol
definition: Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
imported from: envo.owl

environmental material
type: Class
subclass of: material entity
editor preferred term: environmental material
definition: A material entity which other material entities in an environmental system are primarily or partially composed of.
imported from: envo.owl

geographic location
type: Class
subclass of: site
type: NamedIndividual
editor preferred term: geographic location
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: gaz.owl

chromatin
type: Class
subclass of: cellular_component
editor preferred term: chromatin
definition: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
imported from: go.owl

core promoter sequence-specific DNA binding
type: Class
subclass of: molecular_function
subclass of: sequence-specific DNA binding
editor preferred term: core promoter sequence-specific DNA binding
definition: Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
imported from: go.owl

RNA-templated transcription
type: Class
subclass of: cellular process
editor preferred term: RNA-templated transcription
definition: The synthesis of an RNA transcript from an RNA template.
imported from: go.owl

action potential
type: Class
subclass of: biological_process
editor preferred term: action potential
definition: A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
imported from: go.owl

antibody-dependent cellular cytotoxicity
type: Class
subclass of: biological_process
editor preferred term: antibody-dependent cellular cytotoxicity
definition: Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.
imported from: go.owl

type IV hypersensitivity
type: Class
subclass of: hypersensitivity
editor preferred term: type IV hypersensitivity
definition: An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
imported from: go.owl

cytokine production
type: Class
subclass of: biological_process
editor preferred term: cytokine production
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

cell killing
type: Class
subclass of: biological_process
editor preferred term: cell killing
definition: Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
imported from: go.owl

T cell mediated cytotoxicity
type: Class
subclass of: cell killing
editor preferred term: T cell mediated cytotoxicity
definition: The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
imported from: go.owl

startle response
type: Class
subclass of: response to stimulus
subclass of: neuromuscular process
editor preferred term: startle response
definition: An action or movement due to the application of a sudden unexpected stimulus.
imported from: go.owl

regulation of heart rate
type: Class
subclass of: biological_process
editor preferred term: regulation of heart rate
definition: Any process that modulates the frequency or rate of heart contraction.
imported from: go.owl

adaptive immune response
type: Class
subclass of: immune response
editor preferred term: adaptive immune response
definition: An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
imported from: go.owl

cytokine production involved in immune response
type: Class
subclass of: cytokine production
editor preferred term: cytokine production involved in immune response
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

tolerance induction
type: Class
subclass of: biological_process
editor preferred term: tolerance induction
definition: A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
imported from: go.owl

B cell tolerance induction
type: Class
subclass of: tolerance induction
editor preferred term: B cell tolerance induction
definition: A process involving any mechanism for tolerance induction in B cells.
imported from: go.owl

T cell tolerance induction
type: Class
subclass of: tolerance induction
editor preferred term: T cell tolerance induction
definition: A process involving any mechanism for tolerance induction in T cells.
imported from: go.owl

hypersensitivity
type: Class
subclass of: biological_process
editor preferred term: hypersensitivity
definition: An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
imported from: go.owl

cytokine production involved in inflammatory response
type: Class
subclass of: cytokine production
editor preferred term: cytokine production involved in inflammatory response
definition: The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

respiratory system process
type: Class
subclass of: biological_process
editor preferred term: respiratory system process
definition: A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
imported from: go.owl

glomerular filtration
type: Class
subclass of: biological_process
editor preferred term: glomerular filtration
definition: The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein.
imported from: go.owl

molecular_function
type: Class
subclass of: process
editor preferred term: molecular_function
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
imported from: go.owl

antigen binding
type: Class
subclass of: molecular_function
editor preferred term: antigen binding
definition: Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell.
imported from: go.owl

catalytic activity
type: Class
subclass of: molecular_function
editor preferred term: catalytic activity
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
imported from: go.owl

L-iditol 2-dehydrogenase (NAD+) activity
type: Class
subclass of: catalytic activity
editor preferred term: L-iditol 2-dehydrogenase (NAD+) activity
definition: Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. Acts on a number of sugar alcohols, including (but not limited to) L-iditol, D-glucitol, D-xylitol, and D-galactitol.
imported from: go.owl

RNA-directed DNA polymerase activity
type: Class
subclass of: catalytic activity
editor preferred term: RNA-directed DNA polymerase activity
definition: Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1); RNA-template-directed extension of the 3'-end of a DNA strand by one deoxynucleotide at a time.
imported from: go.owl

acetylcholinesterase activity
type: Class
subclass of: catalytic activity
editor preferred term: acetylcholinesterase activity
definition: Catalysis of the reaction: acetylcholine + H2O = choline + acetate.
imported from: go.owl

acyl-CoA oxidase activity
type: Class
subclass of: catalytic activity
editor preferred term: acyl-CoA oxidase activity
definition: Catalysis of the reaction: a 2,3-saturated acyl-CoA + O2 = a (2E)-enoyl-CoA + H2O2.
imported from: go.owl

L-alanine:2-oxoglutarate aminotransferase activity
type: Class
subclass of: catalytic activity
editor preferred term: L-alanine:2-oxoglutarate aminotransferase activity
definition: Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate.
imported from: go.owl

alkaline phosphatase activity
type: Class
subclass of: catalytic activity
editor preferred term: alkaline phosphatase activity
definition: Catalysis of the reaction: a phosphate monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
imported from: go.owl

L-aspartate:2-oxoglutarate aminotransferase activity
type: Class
subclass of: catalytic activity
editor preferred term: L-aspartate:2-oxoglutarate aminotransferase activity
definition: Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate.
imported from: go.owl

cholinesterase activity
type: Class
subclass of: catalytic activity
editor preferred term: cholinesterase activity
definition: Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion.
imported from: go.owl

creatine kinase activity
type: Class
subclass of: catalytic activity
editor preferred term: creatine kinase activity
definition: Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H+.
imported from: go.owl

glutamate dehydrogenase [NAD(P)+] activity
type: Class
subclass of: catalytic activity
editor preferred term: glutamate dehydrogenase [NAD(P)+] activity
definition: Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+.
imported from: go.owl

glutathione transferase activity
type: Class
subclass of: catalytic activity
editor preferred term: glutathione transferase activity
definition: Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
imported from: go.owl

isocitrate dehydrogenase [NAD(P)+] activity
type: Class
subclass of: catalytic activity
editor preferred term: isocitrate dehydrogenase [NAD(P)+] activity
definition: Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H.
imported from: go.owl

lactate dehydrogenase activity
type: Class
subclass of: catalytic activity
editor preferred term: lactate dehydrogenase activity
definition: Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate.
imported from: go.owl

RNA nuclease activity
type: Class
subclass of: catalytic activity
editor preferred term: RNA nuclease activity
definition: Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
imported from: go.owl

monoatomic ion channel activity
type: Class
subclass of: cellular process
editor preferred term: monoatomic ion channel activity
definition: Enables the facilitated diffusion of a monoatomic ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
imported from: go.owl

cellular_component
type: Class
subclass of: material entity
editor preferred term: cellular_component
definition: A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
imported from: go.owl

fibrinogen complex
type: Class
subclass of: protein-containing complex
editor preferred term: fibrinogen complex
definition: A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
imported from: go.owl

chromosome
type: Class
subclass of: cellular_component
editor preferred term: chromosome
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
imported from: go.owl

mitochondrion
type: Class
subclass of: membrane-bounded organelle
editor preferred term: mitochondrion
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
imported from: go.owl

glucose metabolic process
type: Class
subclass of: biological_process
editor preferred term: glucose metabolic process
definition: The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
imported from: go.owl

DNA replication
type: Class
subclass of: biological_process
editor preferred term: DNA replication
definition: The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
imported from: go.owl

chromatin remodeling
type: Class
subclass of: cellular process
editor preferred term: chromatin remodeling
definition: A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication.
imported from: go.owl

phagocytosis
type: Class
subclass of: biological_process
editor preferred term: phagocytosis
definition: A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
imported from: go.owl

immune response
type: Class
subclass of: response to stimulus
editor preferred term: immune response
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl

DNA damage response
type: Class
subclass of: response to stimulus
editor preferred term: DNA damage response
definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
imported from: go.owl

cell cycle
type: Class
subclass of: biological_process
editor preferred term: cell cycle
definition: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
imported from: go.owl

spermatogenesis
type: Class
subclass of: reproductive process
editor preferred term: spermatogenesis
definition: The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa.
imported from: go.owl

blood coagulation
type: Class
subclass of: biological_process
editor preferred term: blood coagulation
definition: The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
imported from: go.owl

learning or memory
type: Class
subclass of: biological_process
editor preferred term: learning or memory
definition: The acquisition and processing of information and/or the storage and retrieval of this information over time.
imported from: go.owl

biological_process
type: Class
subclass of: process
disjoint with: planned process
editor preferred term: biological_process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl

regulation of blood pressure
type: Class
subclass of: biological_process
editor preferred term: regulation of blood pressure
definition: Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
imported from: go.owl

opsonization
type: Class
subclass of: phagocytosis
editor preferred term: opsonization
definition: The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
imported from: go.owl

5'-nucleotidase activity
type: Class
subclass of: catalytic activity
editor preferred term: 5'-nucleotidase activity
definition: Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
imported from: go.owl

cell population proliferation
type: Class
subclass of: biological_process
editor preferred term: cell population proliferation
definition: The multiplication or reproduction of cells, resulting in the expansion of a cell population.
imported from: go.owl

fertilization
type: Class
subclass of: biological_process
editor preferred term: fertilization
definition: The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
imported from: go.owl

cellular process
type: Class
subclass of: biological_process
editor preferred term: cellular process
definition: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
imported from: go.owl

gene expression
type: Class
subclass of: biological_process
editor preferred term: gene expression
definition: The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.
imported from: go.owl

vascular endothelial growth factor production
type: Class
subclass of: cytokine production
editor preferred term: vascular endothelial growth factor production
definition: The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

galactosidase activity
type: Class
subclass of: catalytic activity
editor preferred term: galactosidase activity
definition: Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative.
imported from: go.owl

immunoglobulin mediated immune response
type: Class
subclass of: biological_process
editor preferred term: immunoglobulin mediated immune response
definition: An immune response mediated by immunoglobulins, whether cell-bound or in solution.
imported from: go.owl

amylase activity
type: Class
subclass of: catalytic activity
editor preferred term: amylase activity
definition: Catalysis of the hydrolysis of amylose or an amylose derivative.
imported from: go.owl

beta-N-acetylglucosaminidase activity
type: Class
subclass of: catalytic activity
editor preferred term: beta-N-acetylglucosaminidase activity
definition: Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
imported from: go.owl

hydrolase activity, acting on ester bonds
type: Class
subclass of: catalytic activity
editor preferred term: hydrolase activity, acting on ester bonds
definition: Catalysis of the hydrolysis of any ester bond.
imported from: go.owl

immunoglobulin complex
type: Class
subclass of: protein-containing complex
editor preferred term: immunoglobulin complex
definition: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

B cell receptor complex
type: Class
subclass of: OBI_1110022
editor preferred term: B cell receptor complex
definition: An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
imported from: go.owl

antigen processing and presentation
type: Class
subclass of: biological_process
editor preferred term: antigen processing and presentation
definition: The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
imported from: go.owl

protein domain specific binding
type: Class
subclass of: OBI_0001588
editor preferred term: protein domain specific binding
definition: Binding to a specific domain of a protein.
imported from: go.owl

developmental maturation
type: Class
subclass of: biological_process
editor preferred term: developmental maturation
definition: A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.
imported from: go.owl

reproductive process
type: Class
subclass of: biological_process
editor preferred term: reproductive process
definition: A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
imported from: go.owl

actin filament polymerization
type: Class
subclass of: biological_process
editor preferred term: actin filament polymerization
definition: Assembly of actin filaments by the addition of actin monomers to a filament.
imported from: go.owl

hemopoiesis
type: Class
subclass of: biological_process
editor preferred term: hemopoiesis
definition: The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
imported from: go.owl

cell differentiation
type: Class
subclass of: cellular developmental process
editor preferred term: cell differentiation
definition: The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
imported from: go.owl

connective tissue growth factor production
type: Class
subclass of: cytokine production
editor preferred term: connective tissue growth factor production
definition: The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine production
type: Class
subclass of: cytokine production
editor preferred term: chemokine production
definition: The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
imported from: go.owl

granulocyte macrophage colony-stimulating factor production
type: Class
subclass of: cytokine production
editor preferred term: granulocyte macrophage colony-stimulating factor production
definition: The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

hepatocyte growth factor production
type: Class
subclass of: cytokine production
editor preferred term: hepatocyte growth factor production
definition: The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

type I interferon production
type: Class
subclass of: cytokine production
editor preferred term: type I interferon production
definition: The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
imported from: go.owl

interferon-alpha production
type: Class
subclass of: type I interferon production
editor preferred term: interferon-alpha production
definition: The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interferon-beta production
type: Class
subclass of: cytokine production
editor preferred term: interferon-beta production
definition: The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

type II interferon production
type: Class
subclass of: cytokine production
editor preferred term: type II interferon production
definition: The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
imported from: go.owl

interleukin-1 alpha production
type: Class
subclass of: interleukin-1 production
editor preferred term: interleukin-1 alpha production
definition: The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-1 beta production
type: Class
subclass of: interleukin-1 production
editor preferred term: interleukin-1 beta production
definition: The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-1 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-1 production
definition: The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-10 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-10 production
definition: The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-11 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-11 production
definition: The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-12 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-12 production
definition: The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-13 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-13 production
definition: The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

obsolete interleukin-14 production
type: Class
subclass of: cytokine production
editor preferred term: obsolete interleukin-14 production
definition: OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-15 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-15 production
definition: The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-16 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-16 production
definition: The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-17 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-17 production
definition: The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-18 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-18 production
definition: The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-19 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-19 production
definition: The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-2 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-2 production
definition: The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-20 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-20 production
definition: The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-21 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-21 production
definition: The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-22 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-22 production
definition: The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-23 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-23 production
definition: The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-24 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-24 production
definition: The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-25 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-25 production
definition: The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-26 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-26 production
definition: The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-27 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-27 production
definition: The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-3 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-3 production
definition: The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-4 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-4 production
definition: The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-5 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-5 production
definition: The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-6 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-6 production
definition: The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-7 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-7 production
definition: The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-8 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-8 production
definition: The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-9 production
type: Class
subclass of: cytokine production
editor preferred term: interleukin-9 production
definition: The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

TRAIL production
type: Class
subclass of: cytokine production
editor preferred term: TRAIL production
definition: The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

tumor necrosis factor production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
editor preferred term: tumor necrosis factor production
definition: The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
alternative label: TNF alpha production
imported from: go.owl

lymphotoxin A production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
editor preferred term: lymphotoxin A production
definition: The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A.
alternative label: TNF beta production
imported from: go.owl

transforming growth factor beta1 production
type: Class
subclass of: cytokine production
editor preferred term: transforming growth factor beta1 production
definition: The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

transforming growth factor beta2 production
type: Class
subclass of: cytokine production
editor preferred term: transforming growth factor beta2 production
definition: The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

transforming growth factor beta3 production
type: Class
subclass of: cytokine production
editor preferred term: transforming growth factor beta3 production
definition: The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

protein-containing complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: PR_000000001
editor preferred term: protein-containing complex
example of usage: A ribosome is a protein complex.
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
alternative label: protein complex
imported from: go.owl

macromolecule localization
type: Class
subclass of: biological_process
editor preferred term: macromolecule localization
definition: Any process in which a macromolecule is transported to, or maintained in, a specific location.
imported from: go.owl

DNA polymerase activity
type: Class
subclass of: catalytic activity
editor preferred term: DNA polymerase activity
definition: Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1).
imported from: go.owl

type III interferon production
type: Class
subclass of: cytokine production
editor preferred term: type III interferon production
definition: The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far.
imported from: go.owl

chemokine (C-X-C motif) ligand 9 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-X-C motif) ligand 9 production
definition: The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

helper T cell enhancement of adaptive immune response
type: Class
subclass of: adaptive immune response
editor preferred term: helper T cell enhancement of adaptive immune response
definition: Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
imported from: go.owl

helper T cell enhancement of T cell mediated immune response
type: Class
subclass of: helper T cell enhancement of adaptive immune response
editor preferred term: helper T cell enhancement of T cell mediated immune response
definition: Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
imported from: go.owl

helper T cell enhancement of B cell mediated immune response
type: Class
subclass of: helper T cell enhancement of adaptive immune response
editor preferred term: helper T cell enhancement of B cell mediated immune response
definition: Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
imported from: go.owl

granzyme A production
type: Class
subclass of: biological_process
editor preferred term: granzyme A production
definition: The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

perforin production
type: Class
subclass of: biological_process
editor preferred term: perforin production
definition: The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

granulysin production
type: Class
subclass of: biological_process
editor preferred term: granulysin production
definition: The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-C motif) ligand 20 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 20 production
definition: The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

T cell proliferation
type: Class
subclass of: cell population proliferation
editor preferred term: T cell proliferation
definition: The expansion of a T cell population by cell division. Follows T cell activation.
imported from: go.owl

T cell receptor complex
type: Class
subclass of: OBI_1110022
editor preferred term: T cell receptor complex
definition: A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
imported from: go.owl

T cell activation
type: Class
subclass of: biological_process
editor preferred term: T cell activation
definition: The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
imported from: go.owl

immunoglobulin complex, circulating
type: Class
subclass of: immunoglobulin complex
subclass of: OBI_1110022
editor preferred term: immunoglobulin complex, circulating
definition: An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
alternative label: antibody
imported from: go.owl
IEDB alternative term: antibody

DNA polymerase complex
type: Class
subclass of: protein-containing complex
subclass of: enzyme
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: DNA polymerase activity
editor preferred term: DNA polymerase complex
definition: A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
imported from: go.owl

peptide antigen binding
type: Class
subclass of: antigen binding
editor preferred term: peptide antigen binding
definition: Binding to an antigen peptide.
imported from: go.owl

MHC protein complex
type: Class
subclass of: protein-containing complex
editor preferred term: MHC protein complex
definition: A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
imported from: go.owl
imported from: mro.owl

membrane-bounded organelle
type: Class
subclass of: cellular_component
editor preferred term: membrane-bounded organelle
definition: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
imported from: go.owl

cytotoxic T cell degranulation
type: Class
subclass of: cell killing
editor preferred term: cytotoxic T cell degranulation
definition: The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
imported from: go.owl

sequence-specific DNA binding
type: Class
subclass of: OBI_0001588
editor preferred term: sequence-specific DNA binding
definition: Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
imported from: go.owl

macrophage migration inhibitory factor production
type: Class
subclass of: cytokine production
editor preferred term: macrophage migration inhibitory factor production
definition: The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

oncostatin M production
type: Class
subclass of: cytokine production
editor preferred term: oncostatin M production
definition: The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-C motif) ligand 17 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 17 production
definition: The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

innate immune response
type: Class
subclass of: immune response
editor preferred term: innate immune response
definition: Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
imported from: go.owl

D-glutamyltransferase activity
type: Class
subclass of: catalytic activity
editor preferred term: D-glutamyltransferase activity
definition: Catalysis of the reaction: D-glutamate + D-glutamine = gamma-D-glutamyl-D-glutamate + NH4+. Can also transfer additional glutamyl residues to a peptide, extending the polypeptide chain.
imported from: go.owl

cellular developmental process
type: Class
subclass of: biological_process
editor preferred term: cellular developmental process
definition: A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
imported from: go.owl

multicellular organismal-level homeostasis
type: Class
subclass of: biological_process
editor preferred term: multicellular organismal-level homeostasis
definition: Any process involved in the maintenance of an internal steady state at the level of the multicellular organism.
imported from: go.owl

response to stimulus
type: Class
subclass of: biological_process
editor preferred term: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
imported from: go.owl

neuromuscular process
type: Class
subclass of: biological_process
editor preferred term: neuromuscular process
definition: Any process pertaining to the functions of the nervous and muscular systems of an organism.
imported from: go.owl

chromosome organization
type: Class
subclass of: biological_process
editor preferred term: chromosome organization
definition: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
imported from: go.owl

carboxylic ester hydrolase activity
type: Class
subclass of: catalytic activity
editor preferred term: carboxylic ester hydrolase activity
definition: Catalysis of the hydrolysis of a carboxylic ester bond.
imported from: go.owl

ferritin complex
type: Class
subclass of: protein-containing complex
editor preferred term: ferritin complex
definition: A protein complex that binds iron and acts as a major iron storage system. There are three major subclasses of ferritins: the classical ferritins (Ftn), the heme-containing bacterioferritins (Bfr) and the DNA-binding proteins from starved cells (Dps). Ftn and Bfr are made of 24 subunits, whereas Dps are smaller with 12 subunits. Ftn is found in most kindoms, while Bfr and Dps are restricted to prokaryotes.
imported from: go.owl

actin polymerization-dependent cell motility
type: Class
subclass of: biological_process
editor preferred term: actin polymerization-dependent cell motility
definition: A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell.
imported from: go.owl

transforming growth factor beta production
type: Class
subclass of: cytokine production
editor preferred term: transforming growth factor beta production
definition: The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.
imported from: go.owl

monocyte chemotactic protein-1 production
type: Class
subclass of: chemokine production
editor preferred term: monocyte chemotactic protein-1 production
definition: The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-C motif) ligand 4 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 4 production
definition: The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

macrophage inflammatory protein-1 gamma production
type: Class
subclass of: chemokine production
editor preferred term: macrophage inflammatory protein-1 gamma production
definition: The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

macrophage inflammatory protein-1 alpha production
type: Class
subclass of: chemokine production
editor preferred term: macrophage inflammatory protein-1 alpha production
definition: The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-C motif) ligand 5 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 5 production
definition: The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-C motif) ligand 1 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 1 production
definition: The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

granulocyte colony-stimulating factor production
type: Class
subclass of: cytokine production
editor preferred term: granulocyte colony-stimulating factor production
definition: The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

IP-10 production
type: Class
subclass of: chemokine production
editor preferred term: IP-10 production
definition: The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

granzyme B production
type: Class
subclass of: biological_process
editor preferred term: granzyme B production
definition: The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

tumor necrosis factor superfamily cytokine production
type: Class
subclass of: cytokine production
editor preferred term: tumor necrosis factor superfamily cytokine production
definition: The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

IgG immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
editor preferred term: IgG immunoglobulin complex
definition: A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

IgE immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
editor preferred term: IgE immunoglobulin complex
definition: A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

IgA immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
editor preferred term: IgA immunoglobulin complex
definition: A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

IgM immunoglobulin complex
type: Class
subclass of: immunoglobulin complex
editor preferred term: IgM immunoglobulin complex
definition: A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

chemokine (C-C motif) ligand 22 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 22 production
definition: The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

tumor necrosis factor (ligand) superfamily member 11 production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
editor preferred term: tumor necrosis factor (ligand) superfamily member 11 production
definition: The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-17A production
type: Class
subclass of: interleukin-17 production
editor preferred term: interleukin-17A production
definition: The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

interleukin-17F production
type: Class
subclass of: interleukin-17 production
editor preferred term: interleukin-17F production
definition: The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

complement-dependent cytotoxicity
type: Class
subclass of: cell killing
editor preferred term: complement-dependent cytotoxicity
definition: Cell killing caused by the membrane attack complex formed following complement activation.
imported from: go.owl

histamine secretion mediated by immunoglobulin
type: Class
subclass of: immune response
editor preferred term: histamine secretion mediated by immunoglobulin
definition: Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.
imported from: go.owl

immune complex formation
type: Class
subclass of: immunoglobulin mediated immune response
editor preferred term: immune complex formation
definition: The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus.
imported from: go.owl

immunoglobulin-mediated neutralization
type: Class
subclass of: immunoglobulin mediated immune response
editor preferred term: immunoglobulin-mediated neutralization
definition: The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
imported from: go.owl

chemokine (C-C motif) ligand 19 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 19 production
definition: The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-C motif) ligand 21 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-C motif) ligand 21 production
definition: The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-X-C motif) ligand 12 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-X-C motif) ligand 12 production
definition: The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-X-C motif) ligand 13 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-X-C motif) ligand 13 production
definition: The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

chemokine (C-X-C motif) ligand 16 production
type: Class
subclass of: chemokine production
editor preferred term: chemokine (C-X-C motif) ligand 16 production
definition: The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

amphiregulin production
type: Class
subclass of: cytokine production
editor preferred term: amphiregulin production
definition: The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor.
imported from: go.owl

XCL1 production
type: Class
subclass of: cytokine production
editor preferred term: XCL1 production
definition: The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
imported from: go.owl

Insulin resistance
type: Class
subclass of: disposition
editor preferred term: Insulin resistance
definition: Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
imported from: hp.owl

Neoplasm
type: Class
subclass of: UBERON_0000465
editor preferred term: Neoplasm
definition: An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor).
imported from: hp.owl

conditional specification
type: Class
subclass of: directive information entity
editor preferred term: conditional specification
definition: A directive information entity that specifies what should happen if the trigger condition is fulfilled.
imported from: iao.owl

measurement unit label
type: Class
subclass of: datum label
editor preferred term: measurement unit label
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
imported from: iao.owl

objective specification
type: Class
subclass of: directive information entity
editor preferred term: objective specification
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
imported from: iao.owl

narrative object
type: Class
subclass of: information content entity
editor preferred term: narrative object
definition: A narrative object is an information content entity that is a set of propositions.
imported from: iao.owl

datum label
type: Class
subclass of: information content entity
editor preferred term: datum label
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
imported from: iao.owl

software
type: Class
subclass of: plan specification
editor preferred term: software
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
imported from: iao.owl

data item
type: Class
subclass of: information content entity
editor preferred term: data item
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
imported from: iao.owl
imported from: ogms.owl

symbol
type: Class
subclass of: information content entity
editor preferred term: symbol
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred term: information content entity
definition: A generically dependent continuant that is about some thing.
imported from: iao.owl
imported from: ogms.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001931
editor preferred term: scalar measurement datum
definition: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
imported from: iao.owl

directive information entity
type: Class
subclass of: information content entity
editor preferred term: directive information entity
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
imported from: iao.owl

dot plot
type: Class
subclass of: graph
editor preferred term: dot plot
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
imported from: iao.owl

graph
type: Class
subclass of: figure
editor preferred term: graph
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
imported from: iao.owl

rule
type: Class
subclass of: conditional specification
editor preferred term: rule
definition: A rule is an executable which guides, defines, restricts actions.
imported from: iao.owl

algorithm
type: Class
subclass of: plan specification
editor preferred term: algorithm
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
imported from: iao.owl

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000002
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000124
  one of: IAO_0000125
  one of: IAO_0000423
  one of: IAO_0000428
subclass of: data about an ontology part
editor preferred term: curation status specification
has curation status: IAO_0000125
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: iao.owl

density plot
type: Class
subclass of: graph
editor preferred term: density plot
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
imported from: iao.owl

report
type: Class
subclass of: document
editor preferred term: report
definition: A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).
imported from: iao.owl

data format specification
type: Class
subclass of: directive information entity
editor preferred term: data format specification
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
imported from: iao.owl

data set
type: Class
subclass of: data item
editor preferred term: data set
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
imported from: iao.owl

image
type: Class
subclass of: figure
editor preferred term: image
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
imported from: iao.owl

data about an ontology part
type: Class
subclass of: data item
editor preferred term: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

plan specification
type: Class
subclass of: directive information entity
editor preferred term: plan specification
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
imported from: iao.owl

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001933
editor preferred term: measurement datum
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
imported from: iao.owl

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: OBI_0001909
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is specified output of
  some values from: drawing a conclusion based on data
editor preferred term: conclusion textual entity
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
imported from: iao.owl

material information bearer
type: Class
subclass of: material entity
editor preferred term: material information bearer
definition: A material entity in which a concretization of an information content entity inheres.
imported from: iao.owl

histogram
type: Class
subclass of: graph
editor preferred term: histogram
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
imported from: iao.owl

heatmap
type: Class
subclass of: graph
editor preferred term: heatmap
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
imported from: iao.owl

dendrogram
type: Class
subclass of: graph
editor preferred term: dendrogram
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
imported from: iao.owl

scatter plot
type: Class
subclass of: graph
editor preferred term: scatter plot
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
imported from: iao.owl

obsolescence reason specification
type: Class
equivalent class: Class
  one of: IAO_0000103
  one of: IAO_0000226
  one of: IAO_0000227
  one of: IAO_0000228
  one of: IAO_0000229
  one of: OMO_0001000
subclass of: data about an ontology part
editor preferred term: obsolescence reason specification
has curation status: IAO_0000125
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

textual entity
type: Class
subclass of: information content entity
editor preferred term: textual entity
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
imported from: iao.owl

table
type: Class
subclass of: textual entity
editor preferred term: table
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
imported from: iao.owl

figure
type: Class
subclass of: information content entity
editor preferred term: figure
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
imported from: iao.owl

document
type: Class
subclass of: information content entity
editor preferred term: document
definition: A collection of information content entities intended to be understood together as a whole
imported from: iao.owl

publication
type: Class
subclass of: document
editor preferred term: publication
definition: A document that is the output of a publishing process.
imported from: iao.owl

publication about an investigation
type: Class
subclass of: publication
editor preferred term: publication about an investigation
definition: A publication that is about an investigation
imported from: iao.owl

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: data item
editor preferred term: one dimensional cartesian spatial coordinate datum
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
imported from: iao.owl

length measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred term: length measurement datum
definition: A scalar measurement datum that is the result of measurement of length quality
imported from: iao.owl

denotator type
type: Class
equivalent class: Class
  one of: IAO_0000410
  one of: IAO_0000420
  one of: IAO_0000421
subclass of: data about an ontology part
editor preferred term: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

mass measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred term: mass measurement datum
definition: A scalar measurement datum that is the result of measurement of mass quality
imported from: iao.owl

time measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred term: time measurement datum
definition: A scalar measurement datum that is the result of measuring a temporal interval
imported from: iao.owl

postal address
type: Class
subclass of: textual entity
editor preferred term: postal address
definition: A textual entity that is used as directive to deliver something to a person, or organization
imported from: iao.owl

email address
type: Class
subclass of: information content entity
editor preferred term: email address
imported from: iao.owl

documenting
type: Class
subclass of: planned process
editor preferred term: documenting
definition: A planned process in which a document is created or added to by including the specified input in it.
imported from: iao.owl

line graph
type: Class
subclass of: graph
editor preferred term: line graph
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
imported from: iao.owl

assigning a centrally registered identifier
type: Class
subclass of: planned process
editor preferred term: assigning a centrally registered identifier
definition: A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
imported from: iao.owl

centrally registered identifier symbol
type: Class
subclass of: symbol
editor preferred term: centrally registered identifier symbol
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
imported from: iao.owl

centrally registered identifier registry
type: Class
subclass of: information content entity
editor preferred term: centrally registered identifier registry
definition: A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
imported from: iao.owl

software application
type: Class
subclass of: software
editor preferred term: software application
definition: A software application is software that can be directly executed by some processing unit.
imported from: iao.owl

ontology module
type: Class
subclass of: data about an ontology part
editor preferred term: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative label: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.

base ontology module
type: Class
subclass of: ontology module
editor preferred term: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
type: Class
subclass of: ontology module
editor preferred term: editors ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative label: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred term: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
type: Class
subclass of: ontology module
editor preferred term: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
type: Class
subclass of: subset ontology module
editor preferred term: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred term: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: curation subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

analysis subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: single layer ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative label: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

external import ontology module
type: Class
subclass of: import ontology module
editor preferred term: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

species subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred term: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
type: Class
subclass of: ontology module
editor preferred term: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
type: Class
subclass of: generated ontology module
editor preferred term: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
editor preferred term: taxonomic bridge ontology module

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
editor preferred term: ontology module subsetted by expressivity

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: obo basic subset ontology module
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: ontology module subsetted by OWL profile

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
editor preferred term: EL++ ontology module

pathogenic disposition
type: Class
subclass of: disposition
editor preferred term: pathogenic disposition
definition: A disposition to initiate processes that result in a disorder.
imported from: ido.owl

pathogen
type: Class
subclass of: material entity
editor preferred term: pathogen
definition: A material entity with a pathogenic disposition.
imported from: ido.owl

antibacterial
type: Class
subclass of: material entity
editor preferred term: antibacterial
definition: A material entity bearing an antibacterial disposition.
imported from: ido.owl

infection
type: Class
subclass of: material entity
editor preferred term: infection
definition: A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
imported from: ido.owl

human pathogenicity disposition
type: Class
subclass of: pathogenic disposition
editor preferred term: human pathogenicity disposition
definition: A disposition to initiate processes that result in a disorder in a human organism.
imported from: ido.owl

HLA-DR protein complex
type: Class
subclass of: human MHC class II protein complex
editor preferred term: HLA-DR protein complex
imported from: mro.owl

H2-Db protein complex
type: Class
subclass of: mouse MHC class I protein complex with H2-b haplotype
editor preferred term: H2-Db protein complex
imported from: mro.owl

H2-Dd protein complex
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: H2-Dd protein complex
imported from: mro.owl

H2-IA protein complex
type: Class
subclass of: mouse MHC class II protein complex
editor preferred term: H2-IA protein complex
imported from: mro.owl

H2-IAd protein complex
type: Class
subclass of: H2-IA protein complex
editor preferred term: H2-IAd protein complex
imported from: mro.owl

H2-IAg7 protein complex
type: Class
subclass of: H2-IA protein complex
editor preferred term: H2-IAg7 protein complex
imported from: mro.owl

H2-Kb protein complex
type: Class
subclass of: mouse MHC class I protein complex with H2-b haplotype
editor preferred term: H2-Kb protein complex
imported from: mro.owl

H2-Kd protein complex
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: H2-Kd protein complex
imported from: mro.owl

H2-Ks protein complex
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: H2-Ks protein complex
imported from: mro.owl

H2-Ld protein complex
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: H2-Ld protein complex
imported from: mro.owl

HLA-C protein complex
type: Class
subclass of: human MHC class I protein complex
editor preferred term: HLA-C protein complex
imported from: mro.owl

HLA-DP protein complex
type: Class
subclass of: human MHC class II protein complex
editor preferred term: HLA-DP protein complex
imported from: mro.owl

MHC class I protein complex
type: Class
subclass of: MHC protein complex
editor preferred term: MHC class I protein complex
imported from: mro.owl

MHC class II protein complex
type: Class
subclass of: MHC protein complex
editor preferred term: MHC class II protein complex
imported from: mro.owl

cattle MHC class I protein complex
type: Class
subclass of: MHC class I protein complex
editor preferred term: cattle MHC class I protein complex
imported from: mro.owl

cattle MHC class II protein complex
type: Class
subclass of: MHC class II protein complex
editor preferred term: cattle MHC class II protein complex
imported from: mro.owl

human MHC class I protein complex
type: Class
subclass of: MHC class I protein complex
editor preferred term: human MHC class I protein complex
imported from: mro.owl

human MHC class II protein complex
type: Class
subclass of: MHC class II protein complex
editor preferred term: human MHC class II protein complex
imported from: mro.owl

mouse MHC class I protein complex
type: Class
subclass of: MHC class I protein complex
editor preferred term: mouse MHC class I protein complex
imported from: mro.owl

mouse MHC class II protein complex
type: Class
subclass of: MHC class II protein complex
editor preferred term: mouse MHC class II protein complex
imported from: mro.owl

pig MHC class I protein complex
type: Class
subclass of: MHC class I protein complex
editor preferred term: pig MHC class I protein complex
imported from: mro.owl

mouse MHC protein complex with H2-p haplotype
type: Class
subclass of: MHC protein complex
editor preferred term: mouse MHC protein complex with H2-p haplotype
imported from: mro.owl

HLA protein complex with A2 serotype
type: Class
subclass of: MHC protein complex
editor preferred term: HLA protein complex with A2 serotype
imported from: mro.owl

HLA protein complex with A24 serotype
type: Class
subclass of: MHC protein complex
editor preferred term: HLA protein complex with A24 serotype
imported from: mro.owl

HLA protein complex with A28 serotype
type: Class
subclass of: MHC protein complex
editor preferred term: HLA protein complex with A28 serotype
imported from: mro.owl

HLA protein complex with A29 serotype
type: Class
subclass of: MHC protein complex
editor preferred term: HLA protein complex with A29 serotype
imported from: mro.owl

HLA protein complex with B27 serotype
type: Class
subclass of: MHC protein complex
editor preferred term: HLA protein complex with B27 serotype
imported from: mro.owl

HLA protein complex with DQ3 serotype
type: Class
subclass of: MHC protein complex
editor preferred term: HLA protein complex with DQ3 serotype
imported from: mro.owl

mouse MHC class I protein complex with H2-b haplotype
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: mouse MHC class I protein complex with H2-b haplotype
imported from: mro.owl

rat MHC class I protein complex
type: Class
subclass of: MHC class I protein complex
editor preferred term: rat MHC class I protein complex
imported from: mro.owl

rat MHC class II protein complex with RT1-A haplotype
type: Class
subclass of: MHC class II protein complex
editor preferred term: rat MHC class II protein complex with RT1-A haplotype
imported from: mro.owl

H2-Dq protein complex
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: H2-Dq protein complex
imported from: mro.owl

H2-Kq protein complex
type: Class
subclass of: mouse MHC class I protein complex
editor preferred term: H2-Kq protein complex
imported from: mro.owl

Mus musculus
type: Class
subclass of: Murinae
editor preferred term: Mus musculus
alternative label: house mouse
alternative label: mouse
imported from: ncbitaxon.owl

Rattus norvegicus
type: Class
subclass of: Murinae
editor preferred term: Rattus norvegicus
alternative label: Norway rat
alternative label: brown rat
alternative label: rat
alternative label: rats
imported from: ncbitaxon.owl

Viruses
type: Class
subclass of: OBI_0100026
editor preferred term: Viruses
imported from: ncbitaxon.owl

Cytomegalovirus
type: Class
subclass of: Orthoherpesviridae
editor preferred term: Cytomegalovirus
imported from: ncbitaxon.owl

human gammaherpesvirus 4
type: Class
subclass of: Orthoherpesviridae
editor preferred term: human gammaherpesvirus 4
alternative label: Epstein Barr virus
alternative label: Epstein-Barr virus
alternative label: Epstein-Barr virus EBV
alternative label: Human herpesvirus 4
alternative label: Human herpesvirus 4 (Epstein-Barr virus)
alternative label: Human herpesvirus type 4
imported from: ncbitaxon.owl

Hepatitis B virus
type: Class
subclass of: Revtraviricetes
editor preferred term: Hepatitis B virus
alternative label: Human hepatitis B virus
alternative label: hepatitis B virus (HBV)
alternative label: hepatitis B virus HBV
alternative label: hepatitis B virus, HBV
alternative label: human hepatitis B virus HBV
imported from: ncbitaxon.owl

Flaviviridae
type: Class
subclass of: Kitrinoviricota
editor preferred term: Flaviviridae
alternative label: Flavivirus (arbovirus group B)
imported from: ncbitaxon.owl

Lentivirus
type: Class
subclass of: Revtraviricetes
editor preferred term: Lentivirus
alternative label: Lentivirinae
imported from: ncbitaxon.owl

Human immunodeficiency virus 1
type: Class
subclass of: Lentivirus
editor preferred term: Human immunodeficiency virus 1
alternative label: human immunodeficiency virus 1 HIV-1
alternative label: human immunodeficiency virus HIV-1
alternative label: human immunodeficiency virus type 1 HIV 1
alternative label: human immunodeficiency virus type 1 HIV1
alternative label: human immunodeficiency virus type 1, HIV-1
alternative label: human immunodeficiency virus type I HIV-1
alternative label: human immunodeficiency virus type-1 HIV-1
alternative label: human immunodeficiency virus-1 HIV-1
imported from: ncbitaxon.owl

Human immunodeficiency virus 2
type: Class
subclass of: Lentivirus
editor preferred term: Human immunodeficiency virus 2
alternative label: HIV type 2
alternative label: Human immunodeficiency virus type 2
alternative label: Human immunodeficiency virus-2
alternative label: human immunodeficiency virus type 2 HIV-2
alternative label: human immunodeficiency virus type 2, HIV-2
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Vertebrata <vertebrates>
editor preferred term: Euteleostomi
alternative label: bony vertebrates
imported from: ncbitaxon.owl

Ecdysozoa
type: Class
subclass of: Bilateria
editor preferred term: Ecdysozoa
imported from: ncbitaxon.owl

Dengue virus
type: Class
subclass of: Flaviviridae
editor preferred term: Dengue virus
imported from: ncbitaxon.owl

Treponema pallidum
type: Class
subclass of: Bacteria
editor preferred term: Treponema pallidum
imported from: ncbitaxon.owl

Pancrustacea
type: Class
subclass of: Arthropoda
editor preferred term: Pancrustacea
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: OBI_0100026
editor preferred term: Bacteria
alternative label: eubacteria
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: OBI_0100026
editor preferred term: Archaea
imported from: ncbitaxon.owl

Riboviria
type: Class
subclass of: Viruses
editor preferred term: Riboviria
alternative label: RNA viruses
alternative label: RNA viruses and viroids
imported from: ncbitaxon.owl

Kitrinoviricota
type: Class
subclass of: Riboviria
editor preferred term: Kitrinoviricota
alternative label: Tombus-Noda-like virus sp.
imported from: ncbitaxon.owl

Revtraviricetes
type: Class
subclass of: Riboviria
editor preferred term: Revtraviricetes
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: OBI_0100026
editor preferred term: Eukaryota
alternative label: eucaryotes
alternative label: eukaryotes
imported from: ncbitaxon.owl

Orthoherpesviridae
type: Class
subclass of: Viruses
editor preferred term: Orthoherpesviridae
imported from: ncbitaxon.owl

Hepacivirus hominis
type: Class
subclass of: Flaviviridae
editor preferred term: Hepacivirus hominis
alternative label: Hepacivirus C
alternative label: Hepatitis C virus
alternative label: hepatitis C virus HCV
alternative label: human hepatitis C virus
alternative label: human hepatitis C virus HCV
alternative label: human hepatitis virus C HCV
alternative label: post-transfusion hepatitis non A non B virus
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred term: Euarchontoglires
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred term: Tetrapoda
alternative label: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred term: Amniota
alternative label: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred term: Opisthokonta
imported from: ncbitaxon.owl

Metazoa
type: Class
subclass of: Opisthokonta
editor preferred term: Metazoa
alternative label: metazoans
alternative label: multicellular animals
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Metazoa
editor preferred term: Bilateria
imported from: ncbitaxon.owl

Arabidopsis thaliana
type: Class
subclass of: Eukaryota
editor preferred term: Arabidopsis thaliana
alternative label: mouse-ear cress
alternative label: thale cress
alternative label: thale-cress
imported from: ncbitaxon.owl

Chikungunya virus
type: Class
subclass of: Kitrinoviricota
editor preferred term: Chikungunya virus
imported from: ncbitaxon.owl

HIV-1 group O
type: Class
subclass of: Human immunodeficiency virus 1
editor preferred term: HIV-1 group O
imported from: ncbitaxon.owl

Murinae
type: Class
subclass of: Rodentia
editor preferred term: Murinae
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred term: Mammalia
alternative label: mammals
imported from: ncbitaxon.owl

Dictyostelium discoideum
type: Class
subclass of: Eukaryota
editor preferred term: Dictyostelium discoideum
imported from: ncbitaxon.owl

Ascomycota
type: Class
subclass of: Opisthokonta
editor preferred term: Ascomycota
alternative label: ascomycetes
alternative label: sac fungi
imported from: ncbitaxon.owl

Schizosaccharomyces pombe
type: Class
subclass of: Ascomycota
editor preferred term: Schizosaccharomyces pombe
alternative label: fission yeast
imported from: ncbitaxon.owl

Saccharomyces cerevisiae
type: Class
subclass of: saccharomyceta
editor preferred term: Saccharomyces cerevisiae
alternative label: Saccharomyces cerevisiae 'var. diastaticus'
alternative label: baker's yeast
alternative label: brewer's yeast
imported from: ncbitaxon.owl

Neurospora
type: Class
subclass of: saccharomyceta
editor preferred term: Neurospora
imported from: ncbitaxon.owl

Plasmodium
type: Class
subclass of: Eukaryota
editor preferred term: Plasmodium
imported from: ncbitaxon.owl

Caenorhabditis elegans
type: Class
subclass of: Ecdysozoa
editor preferred term: Caenorhabditis elegans
imported from: ncbitaxon.owl

Arthropoda
type: Class
subclass of: Ecdysozoa
editor preferred term: Arthropoda
alternative label: arthropods
imported from: ncbitaxon.owl

Daphnia
type: Class
subclass of: Pancrustacea
editor preferred term: Daphnia
alternative label: common water fleas
imported from: ncbitaxon.owl

Diptera
type: Class
subclass of: Pancrustacea
editor preferred term: Diptera
alternative label: flies
imported from: ncbitaxon.owl

Culicidae
type: Class
subclass of: Diptera
editor preferred term: Culicidae
alternative label: mosquitos
imported from: ncbitaxon.owl

saccharomyceta
type: Class
subclass of: Ascomycota
editor preferred term: saccharomyceta
imported from: ncbitaxon.owl

Drosophila melanogaster
type: Class
subclass of: Diptera
editor preferred term: Drosophila melanogaster
alternative label: fruit fly
imported from: ncbitaxon.owl

Vertebrata <vertebrates>
type: Class
subclass of: Bilateria
editor preferred term: Vertebrata <vertebrates>
alternative label: Vertebrata
alternative label: vertebrates
imported from: ncbitaxon.owl

Orientia tsutsugamushi
type: Class
subclass of: Bacteria
editor preferred term: Orientia tsutsugamushi
imported from: ncbitaxon.owl

Danio rerio
type: Class
subclass of: Euteleostomi
editor preferred term: Danio rerio
alternative label: leopard danio
alternative label: zebra danio
alternative label: zebra fish
alternative label: zebrafish
imported from: ncbitaxon.owl

Xenopus <genus>
type: Class
subclass of: Tetrapoda
editor preferred term: Xenopus <genus>
alternative label: Xenopus
imported from: ncbitaxon.owl

Gallus gallus
type: Class
subclass of: Amniota
editor preferred term: Gallus gallus
alternative label: Gallus domesticus
alternative label: bantam
alternative label: chicken
alternative label: chickens
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred term: Homo sapiens
alternative label: human
alternative label: human being
imported from: ncbitaxon.owl

Rodentia
type: Class
subclass of: Euarchontoglires
editor preferred term: Rodentia
alternative label: rodent
imported from: ncbitaxon.owl

biological attribute
type: Class
subclass of: quality
editor preferred term: biological attribute
imported from: oba.owl

limb coordination efficacy
type: Class
subclass of: biological attribute
editor preferred term: limb coordination efficacy
definition: The process efficacy of a limb coordination.
imported from: oba.owl

upper limb coordination efficacy
type: Class
subclass of: limb coordination efficacy
editor preferred term: upper limb coordination efficacy
definition: The process efficacy of a upper limb coordination.
imported from: oba.owl

lower limb coordination efficacy
type: Class
subclass of: limb coordination efficacy
editor preferred term: lower limb coordination efficacy
definition: The process efficacy of a lower limb coordination.
imported from: oba.owl

whole organism stability
type: Class
subclass of: biological attribute
editor preferred term: whole organism stability
definition: The stability of a multicellular organism.
imported from: oba.owl

facial muscle performance
type: Class
subclass of: biological attribute
editor preferred term: facial muscle performance
definition: The functionality of a facial muscle.
imported from: oba.owl

peripheral nervous system function
type: Class
subclass of: biological attribute
editor preferred term: peripheral nervous system function
definition: The functionality of a peripheral nervous system.
imported from: oba.owl

knee joint functionality
type: Class
subclass of: biological attribute
editor preferred term: knee joint functionality
definition: The functionality of a knee joint.
imported from: oba.owl

ankle joint functionality
type: Class
subclass of: biological attribute
editor preferred term: ankle joint functionality
definition: The functionality of a ankle joint.
imported from: oba.owl

tendon of biceps brachii functionality
type: Class
subclass of: biological attribute
editor preferred term: tendon of biceps brachii functionality
definition: The functionality of a tendon of biceps brachii.
imported from: oba.owl

brachioradialis functionality
type: Class
subclass of: biological attribute
editor preferred term: brachioradialis functionality
definition: The functionality of a brachioradialis.
imported from: oba.owl

role of being consumer safety officer
type: Class
subclass of: role of regulator of consumables and medical devices
editor preferred term: role of being consumer safety officer
example of usage: Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
example of usage: Person charged with serving as CSO, FDA official who coordinates the review
has curation status: IAO_0000120
definition: the role of a human being that is realized by enforcing regulations to ensure consumer safety
term editor: Jennifer Fostel
term editor: Person:Helen Parkinson
definition source: OBI, CDISC

fluorescent reporter intensity
type: Class
subclass of: measurement datum
editor preferred term: fluorescent reporter intensity
has curation status: IAO_0000125
definition: A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
term editor: person:Chris Stoeckert
definition source: group:OBI
curator note: From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)

regulator role
type: Class
subclass of: regulatory role
editor preferred term: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
has curation status: IAO_0000120
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
term editor: Person:Jennifer Fostel
alternative label: regulator
definition source: OBI

biological feature identification objective
type: Class
subclass of: objective specification
editor preferred term: biological feature identification objective
has curation status: IAO_0000123
definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
term editor: Jennifer Fostel

regulation-assigned role
type: Class
subclass of: regulatory role
editor preferred term: regulation-assigned role
example of usage: Approval letter
has curation status: IAO_0000123
definition: Regulation-assigned role is a regulatory role defined by legislation or governmental orders
term editor: Person: Jennifer Fostel

regulatory role
type: Class
subclass of: role
editor preferred term: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has curation status: IAO_0000120
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
term editor: GROUP: Role branch
definition source: OBI, CDISC
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent

material supplier role
type: Class
subclass of: service provider role
editor preferred term: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
has curation status: IAO_0000120
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
term editor: PERSON:Jennifer Fostel
alternative label: material provider role
alternative label: supplier

contract research organization role
type: Class
subclass of: worker role
editor preferred term: contract research organization role
has curation status: IAO_0000123
definition: a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution
term editor: Person: Jennifer Fostel
alternative label: contract research organization

list-mode data file
type: Class
subclass of: information content entity
editor preferred term: list-mode data file
example of usage: An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
has curation status: IAO_0000125
definition: A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
editor note: One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people.
term editor: person:Chris Stoeckert
definition source: group:Flow Cytometry community

classified data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: class prediction data transformation
subclass of: data set
editor preferred term: classified data set
has curation status: IAO_0000125
definition: A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: data set with assigned class labels

reference substance role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
editor preferred term: reference substance role
example of usage: Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
has curation status: IAO_0000120
definition: a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
term editor: Person:Jennifer Fostel
alternative label: reference substance
definition source: OBI

cytological stain role
type: Class
subclass of: dye role
editor preferred term: cytological stain role
example of usage: haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
has curation status: IAO_0000120
definition: A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization
term editor: Person:Helen Parkinson
term editor: Person:Jennifer Fostel
alternative label: cytological stain

centrifuge pellet role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: OBI_0302886
editor preferred term: centrifuge pellet role
example of usage: Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
has curation status: IAO_0000125
definition: pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..
term editor: GROUP: Role branch
definition source: OBI
curator note: 9Mar09 after discussion with process branch changed definition to include use of centrifuge;

clinical research coordinator role
type: Class
subclass of: worker role
editor preferred term: clinical research coordinator role
has curation status: IAO_0000123
definition: a worker role comprised of handling the administrative duties of a trial or study.
term editor: Person:Jennifer Fostel
alternative label: clinical research coordinator

supernatant role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: OBI_0600014
editor preferred term: supernatant role
example of usage: 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
has curation status: IAO_0000120
definition: 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.
term editor: GROUP: Role branch
definition source: OBI

chromatography column
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has part
  some values from: container
subclass of: Restriction
  on property: has function
  some values from: Class
    intersection of: material separation function
    intersection of: Restriction
      on property: realized in
      all values from: OBI_0600046
editor preferred term: chromatography column
has curation status: IAO_0000123
definition: 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.
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Column_chromatography
curator note: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178

drug role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: molecular entity
editor preferred term: drug role
example of usage: http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
has curation status: IAO_0000120
definition: a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism
term editor: Role Branch
alternative label: drug
definition source: OBI, CDISC

pump valve switch
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: pump valve switch
has curation status: IAO_0000123
definition: A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
editor note: FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
term editor: OBI Instrument branch
definition source: OBI

xenotransplantation
type: Class
subclass of: transplantation
editor preferred term: xenotransplantation
has curation status: IAO_0000125
definition: is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

physical document
type: Class
subclass of: processed material
editor preferred term: physical document
example of usage: a book is a physical document
has curation status: IAO_0000120
definition: A physical document is an object serving as a record of information by means of symbolic marks.
term editor: PERSON: Bjoern Peters
definition source: GROUP: OBI

waiting
type: Class
subclass of: OBI_0600009
editor preferred term: waiting
has curation status: IAO_0000125
definition: A planned process where an agent does not take any new actions towards a particular objective for a period of time until a set of conditions is met.
term editor: PERSON:Alan Ruttenberg
definition source: OBI branch derived
curator note: BP: I have doubts about the utility of this.
curator note: We need a better handling/modeling of time (January 2008)

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is specified output of
    some values from: material processing
subclass of: material entity
editor preferred term: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: IAO_0000122
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

chromatography device
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: material separation function
subclass of: Restriction
  on property: has function
  some values from: environment control function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: chromatography device
has curation status: IAO_0000120
definition: 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.
term editor: Frank Gibson
alternative label: chromatography instrument
definition source: http://en.wikipedia.org/wiki/Chromatography
curator note: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178

mass spectrometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has part
  some values from: mass analyzer
subclass of: Restriction
  on property: has part
  some values from: ion source
subclass of: Restriction
  on property: has part
  some values from: ion detector
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: mass spectrometer
example of usage: LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
has curation status: IAO_0000122
definition: A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry

obsolete_platform
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_platform
has curation status: IAO_0000123
definition: A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
term editor: OBI Instrument branch
definition source: OBI Instrument branch
has obsolescence reason: IAO_0000103
deprecated: true

liquid chromatography mass spectrometry platform
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has part
  some values from: chromatography device
subclass of: Restriction
  on property: has part
  some values from: mass spectrometer
subclass of: Restriction
  on property: has function
  some values from: material separation function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: liquid chromatography mass spectrometry platform
has curation status: IAO_0000123
definition: A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
term editor: OBI instrument branch
definition source: OBI Instrument branch

microarray platform
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has part
  some values from: OBI_0400147
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: microarray platform
has curation status: IAO_0000123
definition: A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
term editor: OBI Instrument branch
definition source: OBI Instrument branch

ratio of collected to emitted light
type: Class
subclass of: measurement datum
editor preferred term: ratio of collected to emitted light
example of usage: 10%
has curation status: IAO_0000120
definition: A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
term editor: person:Chris Stoeckert
term editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

software optimization objective
type: Class
subclass of: software testing objective
editor preferred term: software optimization objective
has curation status: IAO_0000123
definition: Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
term editor: Jennifer Fostel

notified body role
type: Class
subclass of: role of regulator of consumables and medical devices
editor preferred term: notified body role
example of usage: The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
has curation status: IAO_0000120
definition: Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive
editor note: Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB.
term editor: Person: Jennifer Fostel
alternative label: notified body
definition source: OBI, CDISC

allotransplantation
type: Class
subclass of: transplantation
editor preferred term: allotransplantation
has curation status: IAO_0000125
definition: is the transplantation of organs between members of the same species.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

gamma counter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: gamma counter
example of usage: A Geiger counter
has curation status: IAO_0000122
definition: A processed material which measures gamma radiation
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Gamma_counter

trial monitor role
type: Class
subclass of: responsible party role
editor preferred term: trial monitor role
has curation status: IAO_0000123
definition: a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
term editor: Person:Jennifer Fostel
alternative label: trial monitor
curator note: CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study.

positive reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: positive reference substance role
example of usage: MMS mutagen
has curation status: IAO_0000123
definition: 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
term editor: Person: Jennifer Fostel
alternative label: positive reference substance

polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
type: Class
subclass of: molecular entity
editor preferred term: polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
example of usage: PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
has curation status: IAO_0000123
definition: triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia before possible import from CHEBI

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has specified output
      some values from: OBI_0500000
editor preferred term: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: IAO_0000122
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
term editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding achieves objective of drawing conclusion as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
ISA alternative term: study

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: IAO_0000122
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.

reporting party role
type: Class
subclass of: investigation agent role
editor preferred term: reporting party role
example of usage: Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
example of usage: The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
has curation status: IAO_0000120
definition: a study personnel role played by a party who reports the outcome of a study component
editor note: MO:submitter mapped to this term. So, alternative term 'submitter' was added.
term editor: Jennifer Fostel
alternative label: reporting party
alternative label: submitter
definition source: OBI

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
disjoint with: planning
disjoint with: OBI_0200000
disjoint with: OBI_0600013
editor preferred term: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
definition: A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
editor note: Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
term editor: PlanAndPlannedProcess Branch
alternative label: measuring
alternative label: scientific observation
definition source: OBI branch derived
ISA alternative term: study assay
IEDB alternative term: any method

quantitative confidence value
type: Class
subclass of: data item
editor preferred term: quantitative confidence value
has curation status: IAO_0000125
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
term editor: person:Chris Stoeckert
definition source: group:OBI

sample preparation for assay
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: sample preparation for assay
has curation status: IAO_0000125
definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
term editor: PlanAndPlannedProcess Branch
alternative label: study
definition source: OBI branch derived

diagnosis textual entity
type: Class
subclass of: textual entity
editor preferred term: diagnosis textual entity
has curation status: IAO_0000123
definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
term editor: Jennifer Fostel

unplanned occurrence effecting an investigation
type: Class
subclass of: process
editor preferred term: unplanned occurrence effecting an investigation
example of usage: Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
has curation status: IAO_0000120
definition: a process which is external in origin to the investigation that has an impact on the outcome.
term editor: PERSON: Bjoern Peters
definition source: OBI

eMedical record
type: Class
subclass of: information content entity
editor preferred term: eMedical record
has curation status: IAO_0000125
definition: An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
term editor: person:Jennifer Fostel
definition source: article-without-pmid-or-doi:CDISCglossary

culture medium
type: Class
subclass of: processed material
editor preferred term: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: IAO_0000122
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: 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.
term editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI

electronic case report tabulation
type: Class
subclass of: information content entity
editor preferred term: electronic case report tabulation
has curation status: IAO_0000120
definition: An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.
term editor: person:Jennifer Fostel
definition source: CDISC glossary

polystyrene tube
type: Class
subclass of: test tube
editor preferred term: polystyrene tube
example of usage: Polystyrene tubes can be used to contain tissue culture cells during centrifgation
has curation status: IAO_0000122
definition: A polystyrene tube is a test tube made of polystyrene
term editor: PERSON: Chris Stoeckert
definition source: PERSON: Chris Stoeckert

reagent role
type: Class
subclass of: OBI_0003610
editor preferred term: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: IAO_0000120
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
term editor: PERSON:Matthew Brush
alternative label: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

role of regulator of chemical manufacturer
type: Class
subclass of: regulator role
editor preferred term: role of regulator of chemical manufacturer
example of usage: EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
has curation status: IAO_0000120
definition: a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
term editor: Person: Jennifer Fostel
alternative label: regulator of chemical manufacture
definition source: OBI

detector reagent role
type: Class
subclass of: role
editor preferred term: detector reagent role
has curation status: IAO_0000123
definition: a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
editor note: 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
definition source: 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

role of certified IRB professional
type: Class
subclass of: regulation-assigned role
editor preferred term: role of certified IRB professional
example of usage: CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
has curation status: IAO_0000120
definition: 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
term editor: Person:Helen Parkinson
term editor: Person:Jennifer Fostel
alternative label: certified IRB professional
definition source: WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional

patient role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
editor preferred term: patient role
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has curation status: IAO_0000120
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
editor note: See also OMRSE:00000011 'patient role'
term editor: GROUP:Role Branch
alternative label: patient
definition source: OBI, CDISC
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has specified output
  some values from: processed material
subclass of: Restriction
  on property: has specified input
  all values from: material entity
disjoint with: OBI_0600010
editor preferred term: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: IAO_0000122
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative label: material transformation
definition source: OBI branch derived

protocol testing objective
type: Class
subclass of: methodology testing objective
editor preferred term: protocol testing objective
has curation status: IAO_0000123
definition: Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
term editor: Jennifer Fostel

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
editor preferred term: study subject role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: IAO_0000122
definition: 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.
editor note: 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.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS

obsolete_role of being first subject treated
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_role of being first subject treated
example of usage: Rat 1A; first enrolled patient to receive treatment
has curation status: IAO_0000120
definition: 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
term editor: Role Branch
definition source: OBI
has obsolescence reason: IAO_0000103
deprecated: true

measured expression level
type: Class
subclass of: measurement datum
editor preferred term: measured expression level
example of usage: Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
has curation status: IAO_0000120
definition: A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
term editor: person:Chris Stoeckert
definition source: OBI Data Transformation branch

responsible party role
type: Class
subclass of: investigation agent role
editor preferred term: responsible party role
example of usage: he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
has curation status: IAO_0000120
definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
term editor: Person: Jennifer Fostel
alternative label: responsible party
definition source: OBI

principal investigator role
type: Class
subclass of: responsible party role
editor preferred term: principal investigator role
has curation status: IAO_0000123
definition: a responsible party role played by a person responsible for the overall conduct of a study
term editor: Person: Jennifer Fostel
alternative label: principal investigator
curator note: CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)

transplantation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: transplantation
has curation status: IAO_0000125
definition: a protocol application to replace an organ or tissue of an organism
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

obsolete biological vector role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete biological vector role
example of usage: 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
example of usage: 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
has curation status: IAO_0000120
definition: 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.
term editor: GROUP: Role Branch
definition source: OBI and Wikipedia
has obsolescence reason: IAO_0000103
deprecated: true

pH indicator dye role
type: Class
subclass of: dye role
editor preferred term: pH indicator dye role
example of usage: bromophenol blue has a pH indicator dye role
example of usage: phenol red in RPMI; pH=4 indicator dye (also carries reference role)
has curation status: IAO_0000120
definition: the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
term editor: Person: Jennifer Fostel
term editor: Person:Helen Parkinson
alternative label: pH indicator dye

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
editor preferred term: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: IAO_0000122
definition: A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: 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.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1013

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred term: sequence feature identification objective
has curation status: IAO_0000123
definition: Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
term editor: Jennifer Fostel

intervention design
type: Class
equivalent class: Class
  intersection of: OBI_0500000
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: study design independent variable
      intersection of: Restriction
        on property: is about
        some values from: study intervention
subclass of: OBI_0500000
editor preferred term: intervention design
example of usage: 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.
has curation status: IAO_0000125
definition: 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.
term editor: Philppe Rocca-Serra
definition source: OBI branch derived

worker role
type: Class
subclass of: investigation agent role
editor preferred term: worker role
example of usage: Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
has curation status: IAO_0000120
definition: a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
term editor: Person:Jennifer Fostel
alternative label: worker
definition source: OBI

Bernoulli trial
type: Class
subclass of: assay
editor preferred term: Bernoulli trial
has curation status: IAO_0000125
definition: An assay where the output data is a datum with one of two values denoting success and failure.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

gene list
type: Class
subclass of: data set
editor preferred term: gene list
example of usage: Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
has curation status: IAO_0000125
definition: A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
term editor: person:Chris Stoeckert
definition source: group:OBI
curator note: kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.

number of particles in subset
type: Class
subclass of: measurement datum
editor preferred term: number of particles in subset
example of usage: 500, 200, 0
has curation status: IAO_0000120
definition: A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
term editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

number of lost events electronic
type: Class
subclass of: measurement datum
editor preferred term: number of lost events electronic
example of usage: 74, 0, 14 events lost due to data acquisition electronic coincidence.
has curation status: IAO_0000120
definition: A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
term editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

calibration substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: calibration
editor preferred term: calibration substance role
example of usage: pH buffer used to calibrate a pH meter bears a calibration substance role
has curation status: IAO_0000122
definition: 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
term editor: Jennifer Fostel

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred term: molecular feature identification objective
has curation status: IAO_0000123
definition: Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
term editor: Jennifer Fostel

hardware testing objective
type: Class
subclass of: methodology testing objective
editor preferred term: hardware testing objective
has curation status: IAO_0000123
definition: Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
term editor: Jennifer Fostel

incubator
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: incubator
example of usage: Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
has curation status: IAO_0000120
definition: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
term editor: Frank Gibson
definition source: http://www.medterms.com/script/main/art.asp

obsolete_label role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_label role
has curation status: IAO_0000428
definition: Label role is a role which inheres in a material entity and which is realized in a detection of label assay
term editor: Role Branch
alternative label: label
definition source: OBI
has obsolescence reason: IAO_0000228
term replaced by: OBI_0002743
deprecated: true

baseline participant role
type: Class
subclass of: reference subject role
editor preferred term: baseline participant role
example of usage: Subject at time = 0; subject before a stress test.
has curation status: IAO_0000123
definition: a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
term editor: Person: Jennifer Fostel
alternative label: baseline participant

role of independent data monitoring committee
type: Class
subclass of: trial monitor role
editor preferred term: role of independent data monitoring committee
has curation status: IAO_0000120
definition: a trial monitor role charged recommending whether to continue, modify, or end the trial
term editor: Person: Jennifer Fostel
alternative label: independent data monitoring committee

pathologist role
type: Class
subclass of: worker role
editor preferred term: pathologist role
has curation status: IAO_0000123
definition: a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
term editor: Person:Jennifer Fostel
alternative label: Pathologist

supernatant collection system harvesting frame
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
editor preferred term: supernatant collection system harvesting frame
has curation status: IAO_0000120
definition: A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.
term editor: Daniel Schober
definition source: google

filter paper
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
editor preferred term: filter paper
has curation status: IAO_0000120
definition: A device manufacture with the intent to provide a porous unsized paper used for filtering.
term editor: Frank Gibson
definition source: sep:00107

cell co-culturing
type: Class
subclass of: material processing
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: cell
  intersection of: Restriction
    on property: has specified input
    min cardinality: 2
subclass of: Restriction
  on property: has specified input
  some values from: culture medium
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: cell co-culturing
example of usage: Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
has curation status: IAO_0000125
definition: A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

role of Institutional Review Board
type: Class
subclass of: regulator role
editor preferred term: role of Institutional Review Board
example of usage: 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
example of usage: Animal protocol review board
has curation status: IAO_0000120
definition: the role of a organization that is realized by members reviewing study designs for their agreement with regulations
term editor: Person:Helen Parkinson
term editor: Person:Jennifer Fostel
alternative label: Internal Review Board
definition source: OBI, CDISC
curator note: CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial.

eSource document
type: Class
subclass of: information content entity
editor preferred term: eSource document
has curation status: IAO_0000125
definition: an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures
term editor: person:Jennifer Fostel
definition source: article-without-pmid-or-doi:CDISCglossary

crossover population role
type: Class
subclass of: reference subject role
editor preferred term: crossover population role
has curation status: IAO_0000123
definition: a role realized when a participant serves as reference to itself
term editor: Person: Jennifer Fostel
alternative label: crossover population

complete nutrient role
type: Class
subclass of: nutrient role
editor preferred term: complete nutrient role
example of usage: 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
has curation status: IAO_0000123
definition: 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.
term editor: Person: Jennifer Fostel
alternative label: complete nutrient

radiolabel role
type: Class
subclass of: OBI_0002743
editor preferred term: radiolabel role
has curation status: IAO_0000120
definition: a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection
term editor: Jennifer Fostel
alternative label: radiolabel

clonal cDNA library
type: Class
subclass of: recombinant vector
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600064
subclass of: Restriction
  on property: has grain
  some values from: recombinant vector
editor preferred term: cDNA library
example of usage: PMID:6110205. collection of cDNA derived from mouse splenocytes.
has curation status: IAO_0000123
definition: Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
term editor: PERSON: Luisa Montecchi
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: PSI
curator note: PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction

electronic case report form
type: Class
subclass of: information content entity
editor preferred term: electronic case report form
has curation status: IAO_0000120
definition: An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.
term editor: person:Jennifer Fostel
definition source: CDISC glossary

placebo role
type: Class
subclass of: negative reference substance role
editor preferred term: placebo role
example of usage: Pill consisting of inert materials
has curation status: IAO_0000120
definition: 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
term editor: Person:Jennifer Fostel
alternative label: placebo
curator note: 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.

autotransplantation
type: Class
subclass of: transplantation
editor preferred term: autotransplantation
has curation status: IAO_0000125
definition: is the transplantation of tissue from one part of \nthe body to another in the same individual. )
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

parameter threshold
type: Class
subclass of: measurement datum
editor preferred term: parameter threshold
example of usage: 0.01, 0.03
has curation status: IAO_0000120
definition: A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
term editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

study group role
type: Class
subclass of: role
editor preferred term: study group role
example of usage: The group of randomized participants that are assigned to a treatment arm of the trial
has curation status: IAO_0000123
definition: a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
term editor: Jennifer Fostel
alternative label: study group population

p-value
type: Class
subclass of: quantitative confidence value
editor preferred term: p-value
example of usage: PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
has curation status: IAO_0000121
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
editor note: May be outside the scope of OBI long term, is needed so is retained
term editor: PERSON:Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/P-value

population
type: Class
subclass of: material entity
editor preferred term: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: IAO_0000125
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process

NMR 3D molecular structure determination assay
type: Class
equivalent class: Class
  intersection of: OBI_0003117
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: NMR instrument
  intersection of: Restriction
    on property: has specified output
    some values from: 3D structural organization datum
subclass of: OBI_0003117
editor preferred term: NMR 3D molecular structure determination assay
example of usage: Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013).
has curation status: IAO_0000120
definition: A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample.
term editor: IEDB
term editor: PlanAndPlannedProcess Branch
definition source: IEDB

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: image
editor preferred term: imaging assay
has curation status: IAO_0000125
definition: An assay that produces a picture of an entity.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

protocol optimization objective
type: Class
subclass of: protocol testing objective
editor preferred term: protocol optimization objective
has curation status: IAO_0000123
definition: Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
term editor: Jennifer Fostel

role of pathology review board
type: Class
subclass of: worker role
editor preferred term: role of pathology review board
has curation status: IAO_0000123
definition: a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
term editor: Person: Jennifer Fostel
alternative label: pathology review board

microtiter plate
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
editor preferred term: microtiter plate
example of usage: A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
has curation status: IAO_0000122
definition: A microtiter_plate is a flat plate with multiple wells used as small test tubes.
term editor: Melanie Courtot
alternative label: microplate
definition source: http://en.wikipedia.org/wiki/Microtiter_plate

role of impartial witness
type: Class
subclass of: regulation-assigned role
editor preferred term: role of impartial witness
example of usage: According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
has curation status: IAO_0000123
definition: 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
editor note: 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
term editor: Person: Helen Parkinson
term editor: Person: Jennifer Fostel
alternative label: impartial witness

chromatin immunoprecipitation
type: Class
subclass of: immunoprecipitation
editor preferred term: chromatin immunoprecipitation
example of usage: Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.
has curation status: IAO_0000120
definition: An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.
term editor: Bjoern Peters, Randi Vita, James A. Overton
alternative label: ChIP
definition source: OBI

biological replicate role
type: Class
subclass of: reference subject role
editor preferred term: biological replicate role
example of usage: A member of a dose-time group; a patient in a given arm of a trial
has curation status: IAO_0000120
definition: a reference participant role realized by equivalent treatment of participants
term editor: Person:Jennifer Fostel
alternative label: biological replicate
definition source: OBI

radioactivity detection
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has characteristic
        some values from: PATO_0001741
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
subclass of: assay
editor preferred term: radioactivity detection
example of usage: Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material.
has curation status: IAO_0000120
definition: An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
term editor: IEDB
term editor: PlanAndPlannedProcess Branch
definition source: IEDB

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: Restriction
      on property: has characteristic
      some values from: Restriction
        on property: concretizes
        some values from: Restriction
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: investigation
editor preferred term: investigation agent role
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: IAO_0000122
definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
term editor: GROUP: Role Branch
alternative label: investigator
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
ISA alternative term: study person role
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)

nutrient role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
editor preferred term: nutrient role
example of usage: Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
has curation status: IAO_0000120
definition: a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
term editor: GROUP: Role branch
alternative label: nutrient
definition source: Wikipedia, feb 29, 2008
curator note: 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.

obsolete_dropout role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_dropout role
example of usage: Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)
has curation status: IAO_0000120
definition: Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role.
term editor: Role Branch
definition source: OBI
has obsolescence reason: IAO_0000103
deprecated: true

obsolete health care provider role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete health care provider role
has curation status: IAO_0000120
definition: a worker role of providing medical care either within or outside the study timeline
term editor: Person:Jennifer Fostel
alternative label: health care provider
term replaced by: OMRSE_00000012
deprecated: true

methodology testing objective
type: Class
subclass of: objective specification
editor preferred term: methodology testing objective
has curation status: IAO_0000123
definition: Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
term editor: Jennifer Fostel

analytical cytology data file
type: Class
subclass of: information content entity
editor preferred term: analytical cytology data file
example of usage: FCS file, ACS file, foo.fcs, foo.asc
has curation status: IAO_0000125
definition: A digital entity intended to capture data in analytical cytology domain.
term editor: person:Chris Stoeckert
definition source: group:Flow Cytometry community

proxy respondent role
type: Class
subclass of: worker role
editor preferred term: proxy respondent role
has curation status: IAO_0000120
definition: Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
term editor: Jennifer Fostel
alternative label: proxy respondent

fluorescence compensation matrix
type: Class
subclass of: information content entity
editor preferred term: fluorescence compensation matrix
example of usage: ((1.053096, -0.22476), (-0.24877, 1.053096))
has curation status: IAO_0000125
definition: A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.
term editor: person:Chris Stoeckert
definition source: group:Flow Cytometry community

negative reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred term: negative reference substance role
example of usage: Saline solution
has curation status: IAO_0000123
definition: 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
term editor: Person: Jennifer Fostel
alternative label: negative reference substance

role of legally acceptable representative
type: Class
subclass of: regulation-assigned role
editor preferred term: role of legally acceptable representative
example of usage: 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
has curation status: IAO_0000120
definition: 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.
editor note: 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]
term editor: Person: Jennifer Fostel
term editor: Person:Helen Parkinson
alternative label: legally acceptable representative
definition source: OBI, CDISC

investigation results report
type: Class
subclass of: report
editor preferred term: investigation results report
has curation status: IAO_0000125
definition: An investigation report is a report on the results of an investigation.
term editor: person:Chris Stoeckert
definition source: group:OBI

cellular feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred term: cellular feature identification objective
has curation status: IAO_0000123
definition: Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
term editor: Jennifer Fostel

reference subject role
type: Class
subclass of: participant under investigation role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: OBI_0100026
    union of: OBI_0100051
editor preferred term: reference subject role
example of usage: Saline treated rat; one of three identically-treated subjects
has curation status: IAO_0000120
definition: a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
term editor: Jennifer Fostel
alternative label: reference participant
definition source: OBI

vital dye role
type: Class
subclass of: dye role
editor preferred term: vital dye role
example of usage: typtan blue has a vital dye
has curation status: IAO_0000120
definition: A dye role that is realized when used to detect live cells in an experiment
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
term editor: Person: Helen Parkinson
term editor: Person: Jennifer Fostel
alternative label: vital dye

obsolete_blinded medication role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_blinded medication role
example of usage: 115 patients received ipilimumab and blinded medication
example of usage: Inert pill shaped like aspirin tablet
has curation status: IAO_0000120
definition: Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance
term editor: Jennifer Fostel
term editor: Person:Helen Parkinson
has obsolescence reason: IAO_0000103
deprecated: true

sub-investigator role
type: Class
subclass of: worker role
editor preferred term: sub-investigator role
has curation status: IAO_0000123
definition: a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
term editor: Person: Jennifer Fostel
alternative label: sub-investigator
curator note: CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows

data encoding
type: Class
subclass of: documenting
editor preferred term: data encoding
example of usage: storage of measurement results from an assay into a text file, such as
has curation status: IAO_0000120
definition: a documenting process to encode an information entity into a digital document
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE

enzymatic cleavage
type: Class
subclass of: material processing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: characteristic of
      some values from: enzyme
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100051
editor preferred term: enzymatic cleavage
example of usage: Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
has curation status: IAO_0000125
definition: a material processing that digests the fraction of input material that is susceptible to that enzyme
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

hardware optimization objective
type: Class
subclass of: hardware testing objective
editor preferred term: hardware optimization objective
has curation status: IAO_0000123
definition: Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
term editor: Jennifer Fostel

obsolete_defined_material
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_defined_material
has curation status: IAO_0000121
definition: Place holder class, Utility class to gather the defined classes
term editor: Susanna Sansone
definition source: OBI Biomaterial derived
has obsolescence reason: IAO_0000226
deprecated: true

trial statistician role
type: Class
subclass of: worker role
subclass of: Restriction
  on property: realized in
  all values from: Class
    intersection of: investigation
    intersection of: Restriction
      on property: has part
      some values from: Restriction
        on property: realizes
        some values from: Restriction
editor preferred term: trial statistician role
has curation status: IAO_0000123
definition: a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
term editor: Person:Jennifer Fostel
alternative label: trial statistician
curator note: CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9]

standard error
type: Class
subclass of: quantitative confidence value
editor preferred term: standard error
has curation status: IAO_0000125
definition: A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
term editor: person:Chris Stoeckert
definition source: group:OBI
curator note: see P-Value

antigen role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: immune response
editor preferred term: antigen role
has curation status: IAO_0000123
definition: A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors.
editor note: An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens
term editor: Role Branch
definition source: OBI
curator note: 9Mar09 waiting for discussion with immunology terms

software testing objective
type: Class
subclass of: methodology testing objective
editor preferred term: software testing objective
has curation status: IAO_0000123
definition: Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
term editor: Jennifer Fostel

sponsor role
type: Class
subclass of: responsible party role
editor preferred term: sponsor role
has curation status: IAO_0000120
definition: a responsible party role involved with any of the following activities: initiating, managing and funding a study
term editor: Person: Jennifer Fostel
alternative label: sponsor
curator note: CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators

organization
type: Class
subclass of: material entity
editor preferred term: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: IAO_0000122
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

feed role
type: Class
subclass of: complete nutrient role
editor preferred term: feed role
example of usage: 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
has curation status: IAO_0000120
definition: 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.
term editor: Person: Jennifer Fostel
alternative label: feed
definition source: OBI

technical replicate role
type: Class
subclass of: reference subject role
editor preferred term: technical replicate role
example of usage: Aliquots of a tissue subjected to parallel assays
has curation status: IAO_0000123
definition: technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
term editor: Person: Jennifer Fostel
alternative label: technical replicate

dye role
type: Class
subclass of: OBI_0002743
editor preferred term: dye role
has curation status: IAO_0000120
definition: 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.
term editor: Jennifer Fostel
alternative label: dye
definition source: A substance used to color materials www.answers.com/topic/dye 19feb09

cluster
type: Class
subclass of: data set
editor preferred term: cluster
example of usage: Cluster of the lymphocytes population.
has curation status: IAO_0000125
definition: A data set which is a subset of data that are a similar to each other in some way.
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: group:OBI

cohort role
type: Class
subclass of: biological replicate role
editor preferred term: cohort role
example of usage: In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
has curation status: IAO_0000123
definition: a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
term editor: Jennifer Fostel
definition source: WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
definition source: WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
definition source: WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.

artificially induced nucleic acid hybridization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: artificially induced nucleic acid hybridization
example of usage: www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
has curation status: IAO_0000125
definition: Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

DNA extraction
type: Class
subclass of: OBI_0666667
subclass of: Restriction
  on property: has specified output
  some values from: DNA extract
editor preferred term: DNA extraction
has curation status: IAO_0000123
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

plan
type: Class
subclass of: realizable entity
editor preferred term: plan
example of usage: The plan of researcher X to perform an experiment according to a protocol.
has curation status: IAO_0000125
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
editor note: This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
term editor: AR, BP, JM, MC, PRS
definition source: branch derived

obsolete_sample population
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_sample population
example of usage: Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
has curation status: IAO_0000120
definition: A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Philippe Rocca-Serra
alternative label: recruited population
definition source: GROUP: OBI Biomaterial Branch
has obsolescence reason: IAO_0000227
deprecated: true

organism feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred term: organism feature identification objective
has curation status: IAO_0000123
definition: Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
term editor: Jennifer Fostel

number of lost events computer
type: Class
subclass of: measurement datum
editor preferred term: number of lost events computer
example of usage: 0, 125, 787 events lost due to computer busy.
has curation status: IAO_0000120
definition: A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
term editor: person:Kevin Clancy
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt

protocol
type: Class
subclass of: plan specification
editor preferred term: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: IAO_0000122
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
ISA alternative term: study protocol

role of regulator of consumables and medical devices
type: Class
subclass of: regulator role
editor preferred term: role of regulator of consumables and medical devices
example of usage: FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
has curation status: IAO_0000120
definition: a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices
term editor: Person: Jennifer Fostel
alternative label: drug regulatoy authority
definition source: OBI, CDISC

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred term: adding a material entity into a target
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
has curation status: IAO_0000122
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
term editor: BP
definition source: branch derived

analyte role
type: Class
subclass of: OBI_0002444
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
editor preferred term: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: IAO_0000122
definition: A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.

disease stage
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: part of
  some values from: OGMS_0000063
editor preferred term: disease stage
example of usage: Stage II breast cancer, The timepoint of recovery from a disease
has curation status: IAO_0000123
definition: a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
term editor: PERSON: Bjoern peters

intraperitoneal injection
type: Class
equivalent class: Class
  intersection of: intraperitoneal administration
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
subclass of: injection
subclass of: intraperitoneal administration
editor preferred term: intraperitoneal injection
has curation status: IAO_0000123
definition: is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
term editor: BP

precipitate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600034
editor preferred term: precipitate
example of usage: Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
has curation status: IAO_0000120
definition: a precipitate is a material entity which is output of a precipitation process
term editor: PERSON: Philippe Rocca-Serra
alternative label: precipited material
definition source: GROUP: OBI Biomaterial Branch

protein-protein interaction detection assay
type: Class
subclass of: assay
editor preferred term: protein-protein interaction detection assay
has curation status: IAO_0000123
definition: An assay that determines interactions between proteins, such as protein-protein binding.

transcription factor binding site assay
type: Class
subclass of: binding assay
subclass of: Restriction
  on property: has specified output
  some values from: information content entity
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: SO_0000235
editor preferred term: transcription factor binding site assay
example of usage: Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
has curation status: IAO_0000120
definition: An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors
term editor: Philippe Rocca-Serra
alternative label: TF binding
definition source: OBI
term tracker item: https://sourceforge.net/p/obi/obi-terms/767/

obsolete_enrollment
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_enrollment
example of usage: Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
has curation status: IAO_0000125
definition: enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
term editor: Bjoern Peters
definition source: IEDB
has obsolescence reason: IAO_0000227
deprecated: true

adverse event trigger
type: Class
subclass of: conditional specification
editor preferred term: adverse event trigger
has curation status: IAO_0000125
definition: revisit?
term editor: PERSON:Alan Ruttenberg
definition source: OBI branch derived

eluate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: molecular entity
    intersection of: Restriction
      on property: has role
      some values from: OBI_0302732
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302905
editor preferred term: eluate
example of usage: Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
has curation status: IAO_0000120
definition: a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
editor note: need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
term editor: PERSON: Philippe Rocca-Serra
alternative label: eluted material
definition source: OBI Bionaterial

material to be added role
type: Class
subclass of: role
editor preferred term: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: IAO_0000120
definition: 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 is added into another material entity (the target).
term editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch

obsolete_peritoneum
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_peritoneum
has curation status: IAO_0000002
definition: is the serous membrane that forms the lining of the abdominal cavity
has obsolescence reason: IAO_0000228
deprecated: true

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: data item
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0001909
editor preferred term: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: IAO_0000122
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred term: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: IAO_0000122
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch

obsolete_documenting
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_documenting
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: IAO_0000125
term editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has obsolescence reason: IAO_0000228
term replaced by: documenting
deprecated: true

histological sample preparation
type: Class
subclass of: material processing
subclass of: specimen collection process
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100066
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400168
editor preferred term: histological sample preparation
has curation status: IAO_0000125
definition: histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
term editor: PERSON:Bjoern Peters
definition source: OBI branch derived

inductive reasoning
type: Class
subclass of: drawing a conclusion based on data
editor preferred term: inductive reasoning
example of usage: Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
has curation status: IAO_0000428
definition: a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
editor note: BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. Proposal is to obsolete.
term editor: Bjoern Peters
definition source: wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning

mass analyzer
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: mass analyzer
example of usage: The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
has curation status: IAO_0000120
definition: A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
term editor: Frank Gibson
term editor: PERSON: Daniel Schober
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer

hypothesis-driven investigation
type: Class
subclass of: investigation
editor preferred term: hypothesis-driven investigation
has curation status: IAO_0000125
definition: is an investigation with the goal to test one or more hypothesis
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

hypothesis generating investigation
type: Class
subclass of: investigation
editor preferred term: hypothesis generating investigation
has curation status: IAO_0000125
definition: is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

ion source
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: ionization function
editor preferred term: ion source
example of usage: The ion source of a Voyager-DE??? STR Biospectrometry Workstation
has curation status: IAO_0000122
definition: An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source

ion detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: ion detector
example of usage: The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
has curation status: IAO_0000122
definition: An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Detector

metabolite profiling assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100051
editor preferred term: metabolite profiling assay
example of usage: Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
has curation status: IAO_0000120
definition: An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism
term editor: Philippe Rocca-Serra
alternative label: metabolite assay
alternative label: metabolomic assay
definition source: OBI

light emission function
type: Class
subclass of: excitation function
editor preferred term: light emission function
has curation status: IAO_0000122
definition: A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

record function
type: Class
subclass of: function
editor preferred term: record function
has curation status: IAO_0000122
definition: A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

magnify function
type: Class
subclass of: function
editor preferred term: magnify function
has curation status: IAO_0000122
definition: A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

contain function
type: Class
subclass of: function
editor preferred term: contain function
example of usage: A syringe, a beaker
has curation status: IAO_0000122
definition: A contain function is a function to constrain a material entities location in space
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

heat function
type: Class
subclass of: function
editor preferred term: heat function
has curation status: IAO_0000122
definition: A heat function is a function that increases the internal kinetic energy of a material
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

material separation function
type: Class
subclass of: function
editor preferred term: material separation function
has curation status: IAO_0000122
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

ionize process
type: Class
subclass of: material processing
subclass of: Restriction
  on property: realizes
  some values from: ionization function
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has participant
  some values from: material entity
editor preferred term: ionize process
example of usage: Electrospray ionization in mass spectrometry
has curation status: IAO_0000123
definition: 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.
editor note: 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
term editor: Person:Bjoern Peters

excitation function
type: Class
subclass of: function
editor preferred term: excitation function
has curation status: IAO_0000122
definition: A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

freeze function
type: Class
subclass of: function
editor preferred term: freeze function
has curation status: IAO_0000122
definition: A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

synthesizing function
type: Class
subclass of: function
editor preferred term: synthesizing function
has curation status: IAO_0000122
definition: 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.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

perturb function
type: Class
subclass of: function
editor preferred term: perturb function
has curation status: IAO_0000122
definition: A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Perturbation_biology

filter function
type: Class
subclass of: material separation function
editor preferred term: filter function
has curation status: IAO_0000122
definition: A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
term editor: Frank Gibson

mechanical function
type: Class
subclass of: function
editor preferred term: mechanical function
has curation status: IAO_0000122
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Mechanical_work

gas filter function
type: Class
subclass of: filter function
editor preferred term: gas filter function
has curation status: IAO_0000122
definition: A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
term editor: Frank Gibson

liquid filter function
type: Class
subclass of: filter function
editor preferred term: liquid filter function
has curation status: IAO_0000122
definition: A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
term editor: Frank Gibson

transfer function
type: Class
subclass of: function
editor preferred term: transfer function
has curation status: IAO_0000122
definition: A transfer function is a function to displace a material from one location to another.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

electricity supply function
type: Class
subclass of: energy supply function
editor preferred term: electricity supply function
example of usage: the function of supplying current during a neuroscience experiment.
has curation status: IAO_0000122
definition: An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
alternative label: power supply

ionization function
type: Class
subclass of: function
editor preferred term: ionization function
example of usage: The ion source in amass spectrometer
has curation status: IAO_0000122
definition: An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Ionization

cool function
type: Class
subclass of: function
editor preferred term: cool function
has curation status: IAO_0000122
definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

connection function
type: Class
subclass of: function
editor preferred term: connection function
example of usage: An electricity cable
has curation status: IAO_0000122
definition: A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

isoelectric focusing device
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: transfer function
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: isoelectric focusing device
has curation status: IAO_0000120
definition: An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated.
term editor: Frank Gibson
alternative label: isoelectric focusing unit
definition source: sep:00097

thermostatic circulator
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: thermostatic circulator
has curation status: IAO_0000120
definition: A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid
term editor: Frank Gibson
definition source: sep:00098

energy supply function
type: Class
subclass of: function
editor preferred term: energy supply function
has curation status: IAO_0000122
definition: An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
term editor: Frank Gibson

information processor function
type: Class
subclass of: function
subclass of: Restriction
  on property: has part
  some values from: measure function
subclass of: Restriction
  on property: has part
  some values from: consume data function
editor preferred term: information processor function
has curation status: IAO_0000122
definition: An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
term editor: Frank Gibson
alternative label: data processor function

signal conversion function
type: Class
subclass of: information processor function
editor preferred term: signal conversion function
has curation status: IAO_0000122
definition: A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
alternative label: transduction function

blot module
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: blot module
has curation status: IAO_0000123
definition: A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
term editor: Frank Gibson
definition source: sep:00092

signal amplification function
type: Class
subclass of: signal conversion function
editor preferred term: signal amplification function
has curation status: IAO_0000122
definition: A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

image acquisition function
type: Class
subclass of: measure function
subclass of: Restriction
  on property: characteristic of
  some values from: image creation device
subclass of: Restriction
  on property: realized in
  all values from: image creation
editor preferred term: image acquisition function
has curation status: IAO_0000122
definition: An image acquisition function is a function to acquire an image of a material
term editor: Frank Gibson

image creation device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: image acquisition function
subclass of: measurement device
editor preferred term: image acquisition device
has curation status: IAO_0000123
definition: An image creation device is a device which captures a digitized image of an object
term editor: Frank Gibson
alternative label: image acquisition device
definition source: sep:00096

solid support function
type: Class
subclass of: function
editor preferred term: solid support function
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
has curation status: IAO_0000122
definition: A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

display function
type: Class
subclass of: information processor function
editor preferred term: display function
has curation status: IAO_0000122
definition: A display function is a function to present information by translating that information through some lookup process into visual form.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

environment control function
type: Class
subclass of: function
editor preferred term: environment control function
has curation status: IAO_0000122
definition: An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

sort function
type: Class
subclass of: material separation function
editor preferred term: sort function
has curation status: IAO_0000122
definition: A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot

gel dryer
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: gel dryer
has curation status: IAO_0000120
definition: A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
term editor: Frank Gibson
definition source: sep:00094

primer role
type: Class
subclass of: complementary nucleotide probe role
subclass of: Restriction
  on property: realized in
  all values from: polymerase chain reaction
editor preferred term: primer role
has curation status: IAO_0000123
definition: 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.
definition source: (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

PCR product
type: Class
equivalent class: Class
  intersection of: double-stranded DNA
  intersection of: Restriction
    on property: is specified output of
    some values from: polymerase chain reaction
subclass of: double-stranded DNA
subclass of: amplified DNA
editor preferred term: PCR product
example of usage: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
has curation status: IAO_0000122
definition: is double stranded DNA that is the specified output of a polymerase chain reaction
editor note: We are using PCR and not the written out words, as this is the most common used.
term editor: GROUP: OBI BIomaterial Branch
definition source: GROUP: OBI BIomaterial Branch

viral RNA extraction
type: Class
subclass of: OBI_0666666
subclass of: Restriction
  on property: has specified input
  some values from: Viruses
editor preferred term: viral RNA extraction
example of usage: 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
has curation status: IAO_0000123
definition: The extraction of RNA from an input material that specifically isolates viral RNA
term editor: Person:Bjoern Peters

nucleic acid template role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: characteristic of
  some values from: nucleic acid
subclass of: Restriction
  on property: realized in
  all values from: polymerase chain reaction
editor preferred term: nucleic acid template role
example of usage: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
has curation status: IAO_0000123
definition: 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.

recombinant plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600064
subclass of: plasmid
subclass of: recombinant vector
editor preferred term: recombinant plasmid
has curation status: IAO_0000120
definition: a plasmid in which extraneous DNA has been inserted.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Kevin Clancy
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI Biomaterial Branch

cloning vector role
type: Class
subclass of: material to be added role
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: nucleic acid
  intersection of: Restriction
    on property: realized in
    all values from: OBI_0600064
editor preferred term: cloning vector role
example of usage: pBluescript plays the role of a cloning vector
has curation status: IAO_0000123
definition: A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
editor note: JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/
term editor: PERSON: Helen Parkinson

cell cycle synchronization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: cell cycle synchronization
example of usage: Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
has curation status: IAO_0000120
definition: a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
term editor: OBI PA
definition source: Bjoern Peters and Nicole Washington

polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: synthesizing function
    intersection of: Restriction
      on property: characteristic of
      some values from: DNA polymerase complex
subclass of: Restriction
  on property: has specified input
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: PCR product
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: polymerase chain reaction
example of usage: Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
has curation status: IAO_0000123
definition: PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
term editor: OBI Plan
alternative label: PCR
definition source: adapted from wikipedai

cloning insert role
type: Class
subclass of: role
editor preferred term: cloning insert role
has curation status: IAO_0000121
definition: cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
editor note: Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
term editor: GROUP: Role branch
definition source: OBII and Wikipedia

measuring glucose concentration in blood serum assay
type: Class
subclass of: OBI_0003040
subclass of: OBI_2100020
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100017
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: glucose
  intersection of: Restriction
    on property: has specified input
    some values from: glucose
editor preferred term: measuring glucose concentration in blood serum assay
example of usage: Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319.
has curation status: IAO_0000123
definition: An assay that determines the concentration of glucose molecules in a blood serum sample
term editor: Bjoern Peters
definition source: OBI

reverse transcriptase
type: Class
equivalent class: Class
  intersection of: enzyme
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: RNA-directed DNA polymerase activity
subclass of: enzyme
editor preferred term: reverse transcriptase
has curation status: IAO_0000125
definition: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
term editor: person:Melanie Courtot
definition source: group:OBI

obsolete_trypsinized material
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_trypsinized material
example of usage: A trypsinized suspension of cells
has curation status: IAO_0000002
definition: A material entity that has undergone a process of digestion with trypsin
term editor: Person:Bjoern Peters
has obsolescence reason: IAO_0000103
deprecated: true

syringe
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: syringe
example of usage: Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
has curation status: IAO_0000122
definition: A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
term editor: Philippe Rocca-Serra
definition source: OBI Instrument adapted from Wikipedia

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302884
editor preferred term: extract
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
has curation status: IAO_0000120
definition: an extract is a material entity which results from an extraction process
term editor: PERSON: Philippe Rocca-Serra
alternative label: extracted material
definition source: GROUP: OBI Biomatrial Branch

transcription profiling assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: RNA extract
        intersection of: Restriction
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: analyte role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: ribonucleic acid
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100051
      intersection of: Restriction
        on property: has part
        some values from: ribonucleic acid
  intersection of: Restriction
    on property: has specified output
    some values from: measurement datum
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: gene expression
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: transcription profiling identification objective
subclass of: assay
editor preferred term: transcription profiling assay
example of usage: Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
has curation status: IAO_0000120
definition: An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
editor note: This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term.
term editor: Philippe Rocca-Serra
alternative label: gene expression profiling
alternative label: transcription profiling
definition source: OBI

averaging objective
type: Class
subclass of: OBI_0200166
editor preferred term: averaging objective
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
has curation status: IAO_0000122
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi

injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred term: injection
example of usage: Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
has curation status: IAO_0000120
definition: injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
term editor: Philippe Rocca-Serra
definition source: OBI Biomaterial

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acid
    union of: protein-containing complex
    union of: PR_000000001
    union of: Restriction
      on property: has part
      some values from: ribonucleic acid
    union of: Restriction
      on property: has part
      some values from: protein-containing complex
    union of: Restriction
      on property: has part
      some values from: PR_000000001
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: catalytic activity
subclass of: material entity
editor preferred term: enzyme
has curation status: IAO_0000125
definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
editor note: MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
term editor: person: Melanie Courtot
definition source: GROUP:OBI

intraperitoneal administration
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0002358
subclass of: OBI_0600007
editor preferred term: intraperitoneal administration
example of usage: Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
has curation status: IAO_0000123
definition: The administration of a substance into the peritoneum of an organism
term editor: Person:Bjoern Peters

plasmid
type: Class
equivalent class: Class
  intersection of: double-stranded DNA
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: gene expression
  intersection of: Restriction
    on property: has quality
    some values from: SO_0000988
subclass of: double-stranded DNA
editor preferred term: plasmid
has curation status: IAO_0000125
definition: plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
term editor: person:Melanie Courtot
definition source: group:OBI

injection into organ section
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: OBI_0100066
subclass of: injection
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred term: injection into organ section
example of usage: Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
has curation status: IAO_0000123
definition: A process in which an input substance is injected into a organ section.
term editor: Person:Bjoern Peters

polyacrylamide gel
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has part
  some values from: acrylamide
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302890
editor preferred term: polyacrylamide gel
example of usage: Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
has curation status: IAO_0000120
definition: a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
term editor: PERSON: Jie Zheng
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch

DNA sequence feature detection assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
editor preferred term: DNA sequence feature detection assay
example of usage: genotyping using an Affymetrix chip
has curation status: IAO_0000123
definition: An assay with the objective to determine a sequence feature of DNA
term editor: Bjoern Peters
term editor: Philippe Rocca-Serra
definition source: OBI

adding material objective
type: Class
subclass of: material combination objective
editor preferred term: adding material objective
example of usage: creating a mouse infected with LCM virus
has curation status: IAO_0000122
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
term editor: BP

genotyping assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: genotype information
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
editor preferred term: genotyping assay
example of usage: High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
has curation status: IAO_0000120
definition: An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
term editor: Philippe Rocca-Serra
alternative label: SNP analysis
alternative label: genotype profiling
definition source: OBI Biomaterial

needle
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: needle
example of usage: Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
has curation status: IAO_0000120
definition: A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
term editor: Philippe Rocca-Serra
definition source: OBI Instrument

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred term: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: IAO_0000122
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
term editor: PERSON: Bjoern Peters
definition source: PPPB branch

DNA sequence variation detection assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: DNA extract
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
editor preferred term: DNA sequence variation detection assay
example of usage: Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
has curation status: IAO_0000122
definition: An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule.
term editor: Philippe Rocca-Serra
definition source: OBI Biomaterial

agarose gel
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302890
editor preferred term: agarose gel
example of usage: Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
has curation status: IAO_0000120
definition: a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch

assay objective
type: Class
subclass of: objective specification
editor preferred term: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: IAO_0000122
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
term editor: PPPB branch
definition source: PPPB branch

obsolete_heart
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_heart
example of usage: Alan Ruttenberg's heart
has curation status: IAO_0000002
definition: The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
term editor: Person:Bjoern Peters
definition source: http://en.wikipedia.org/wiki/Heart
has obsolescence reason: IAO_0000230
deprecated: true

analyte assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
editor preferred term: analyte assay
example of usage: example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
has curation status: IAO_0000122
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
term editor: Alan Ruttenberg
term editor: Bjoern Peters
term editor: Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: Alan Ruttenberg
definition source: Bjoern Peters
definition source: Helen Parkinson
definition source: OBI Planned process branch
definition source: Philippe Rocca-Serra

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
editor preferred term: target of material addition role
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has curation status: IAO_0000120
definition: 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.
editor note: 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.
term editor: GROUP: Role Branch
definition source: OBI

mass measurement assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: material entity
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: mass measurement datum
editor preferred term: mass measurement assay
example of usage: The patients was weighed and mass was determined to be 47 kilograms
has curation status: IAO_0000120
definition: An assay that determines the mass of an evaluant
term editor: Helen Parkinson
definition source: OBI

obsolete_identification
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_identification
example of usage: DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
has curation status: IAO_0000124
definition: a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
term editor: Philippe Rocca-Serra
has obsolescence reason: IAO_0000103
deprecated: true

intracellular electrophysiology recording assay
type: Class
subclass of: OBI_0002176
subclass of: Restriction
  on property: has specified output
  some values from: mass measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: monoatomic ion channel activity
editor preferred term: intracellular electrophysiology recording assay
has curation status: IAO_0000123
definition: An electrophysiology assay where the recording location of the electrode is intracellular.
term editor: Frank Gibson
definition source: Frank Gibson

packed column
type: Class
subclass of: chromatography column
editor preferred term: packed column
has curation status: IAO_0000120
definition: A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
term editor: PERSON:Daniel Schober
definition source: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218

obsolete_defined_output
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_defined_output
example of usage: example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation.
has curation status: IAO_0000121
definition: This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
has obsolescence reason: IAO_0000226
deprecated: true

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
editor preferred term: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: IAO_0000122
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator

normalized data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200169
subclass of: data set
editor preferred term: normalized data set
has curation status: IAO_0000125
definition: A data set that is produced as the output of a normalization data transformation.
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has specified output
    some values from: measurement datum
editor preferred term: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: IAO_0000122
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson

extracellular electrophysiology recording assay
type: Class
subclass of: OBI_0002176
subclass of: Restriction
  on property: has specified output
  some values from: mass measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: monoatomic ion channel activity
editor preferred term: extracellular electrophysiology recording assay
example of usage: The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
has curation status: IAO_0000120
definition: An electrophysiology assay where the recording location of the electrode is extracellular.
term editor: Frank Gibson
term editor: Helen Parkinson
definition source: Frank Gibson

consume data function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: material entity
editor preferred term: consume data function
has curation status: IAO_0000122
definition: Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
term editor: PERSON: Daniel Schober
term editor: PERSON: Frank Gibson
term editor: PERSON: Melanie Courtot

material transformation objective
type: Class
subclass of: objective specification
editor preferred term: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: IAO_0000122
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative label: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: processed material
editor preferred term: manufacturing
has curation status: IAO_0000122
definition: A planned process with the objective to produce a processed material which will have a function for future use.
editor note: A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred term: manufacturing objective
has curation status: IAO_0000122
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

column chromatography detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: column chromatography detector
has curation status: IAO_0000120
definition: There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
curator note: chromatography detector, defined class/xps

Bruker autosampler
type: Class
subclass of: autosampler
editor preferred term: Bruker autosampler
has curation status: IAO_0000120
definition: A Bruker autosampler is an autosampler made by Bruker.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209

organic acid column
type: Class
subclass of: chromatography column
editor preferred term: organic acid column
has curation status: IAO_0000120
definition: An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099

thermal conductivity detector
type: Class
subclass of: gas chromatography detector
editor preferred term: thermal conductivity detector
has curation status: IAO_0000120
definition: The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity).
term editor: PERSON:Daniel Schober
alternative label: TCD, hot wire detector
definition source: WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084

Bruker US 2 NMR magnet
type: Class
subclass of: Bruker NMR magnet
editor preferred term: Bruker US 2 NMR magnet
has curation status: IAO_0000120
definition: An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
curator note: NMR instrument

protein column
type: Class
subclass of: chromatography column
editor preferred term: protein column
has curation status: IAO_0000120
definition: A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
curator note: refactor as defined class

solvent mixer
type: Class
subclass of: chromatography instrument
editor preferred term: solvent mixer
has curation status: IAO_0000120
definition: A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072

mass spectrometry assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: mass spectrometer
subclass of: assay
editor preferred term: mass spectrometry assay
example of usage: Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.
has curation status: IAO_0000120
definition: An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles.
term editor: Philippe Rocca-Serra
definition source: Philippe Rocca-Serra

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: OBI_0500000
subclass of: planned process
editor preferred term: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: IAO_0000122
definition: a planned process that carries out a study design
editor note: 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.
definition source: branch derived
curator note: 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.

Bruker NMR Case sample changer
type: Class
subclass of: Bruker autosampler
editor preferred term: Bruker NMR Case sample changer
has curation status: IAO_0000120
definition: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
curator note: NMR instrument

nano pump system
type: Class
subclass of: chromatography pump system
editor preferred term: nano pump system
has curation status: IAO_0000120
definition: A pump system optimized for nano flow chromatography.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052

Bruker AutoClean system
type: Class
subclass of: NMR tube washing system
editor preferred term: Bruker AutoClean system
has curation status: IAO_0000120
definition: NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
editor note: washing system/NMR tube washing system, XPS: device has function washing
term editor: PERSON:Daniel Schober
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205

manual injection system
type: Class
subclass of: sample injection system
editor preferred term: manual injection system
has curation status: IAO_0000120
definition: The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064

Varian GEMINI spectrometer
type: Class
subclass of: Varian NMR instrument
editor preferred term: Varian GEMINI spectrometer
has curation status: IAO_0000120
definition: An older Varian Broadband NMR spectrometer.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
curator note: NMR instrument

column connector
type: Class
subclass of: chromatography device
editor preferred term: column connector
has curation status: IAO_0000120
definition: A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
curator note: chromatography device

solid NMR probe
type: Class
subclass of: NMR probe
editor preferred term: solid NMR probe
has curation status: IAO_0000120
definition: An NMR probe that is designed to hold a solid sample.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
curator note: NMR device

Bruker high resolution probe
type: Class
subclass of: Bruker NMR probe
editor preferred term: Bruker high resolution probe
has curation status: IAO_0000120
definition: BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.
term editor: PERSON:Daniel Schober
alternative label: HR Probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223
curator note: NMR probe

chromatography detector
type: Class
subclass of: chromatography instrument
editor preferred term: chromatography detector
has curation status: IAO_0000120
definition: A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012

normal phase column
type: Class
subclass of: chromatography column
editor preferred term: normal phase column
has curation status: IAO_0000120
definition: A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097

APOLLO console
type: Class
subclass of: tecmag NMR console
editor preferred term: APOLLO console
has curation status: IAO_0000120
definition: The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.tecmag.com/apollo.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
curator note: NMR instrument/NMR console

NMR sample holder
type: Class
subclass of: device
editor preferred term: NMR sample holder
has curation status: IAO_0000120
definition: An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
curator note: NMR device

chromatography instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
editor preferred term: chromatography instrument
has curation status: IAO_0000120
definition: Any instrument that is used to carry out a chromatography experiment.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
curator note: chromatography device, defined class?

continuous wave NMR instrument
type: Class
subclass of: NMR instrument
editor preferred term: continuous wave NMR instrument
has curation status: IAO_0000120
definition: Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
curator note: NMR instrument

fourier transformation NMR instrument
type: Class
subclass of: NMR instrument
editor preferred term: fourier transformation NMR instrument
has curation status: IAO_0000120
definition: In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
curator note: NMR instrument

nitrogen phosphorous detector
type: Class
subclass of: gas chromatography detector
editor preferred term: nitrogen phosphorous detector
has curation status: IAO_0000120
definition: The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089

cation exchange column
type: Class
subclass of: ion exchange column
editor preferred term: cation exchange column
has curation status: IAO_0000120
definition: A cation exchange column is a chromatography column that is used in cation exchange chromatography.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096

direct detection NMR probe
type: Class
subclass of: NMR probe
editor preferred term: direct detection NMR probe
has curation status: IAO_0000120
definition: An NMR probe designed to allow the direct detection of acquisition nuclei.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
curator note: NMR device

Bruker B-ACS system
type: Class
subclass of: Bruker autosampler
editor preferred term: Bruker B-ACS system
has curation status: IAO_0000120
definition: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
curator note: NMR instrument

rapid resolution column
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
editor preferred term: rapid resolution column
has curation status: IAO_0000120
definition: A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102

liquid chromatography autosampler
type: Class
subclass of: chromatography instrument
editor preferred term: liquid chromatography autosampler
has curation status: IAO_0000120
definition: Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061

vacuum degasser
type: Class
subclass of: chromatography pump system
editor preferred term: vacuum degasser
has curation status: IAO_0000120
definition: A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/vacuum.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053

capillary column
type: Class
subclass of: chromatography column
editor preferred term: capillary column
has curation status: IAO_0000120
definition: A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066

sample inlet
type: Class
subclass of: chromatography device
editor preferred term: sample inlet
has curation status: IAO_0000120
definition: The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
curator note: chromatography device

NMR tube washing system
type: Class
subclass of: device
editor preferred term: NMR tube washing system
has curation status: IAO_0000120
definition: An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
curator note: NMR instrument

NMR console
type: Class
subclass of: device
editor preferred term: NMR console
has curation status: IAO_0000125
definition: A component of an NMR instrument that controls the activities of the other components.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
curator note: NMR instrument, TODO: same as or part of acquisition computer?

dual loop autosampler
type: Class
subclass of: liquid chromatography autosampler
editor preferred term: dual loop autosampler
has curation status: IAO_0000120
definition: A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063

variable wavelength detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: variable wavelength detector
has curation status: IAO_0000120
definition: A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079

Bruker LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker LC-NMR platform
has curation status: IAO_0000120
definition: The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
curator note: NMR instrument
curator note: hyphenated NMR instrument platform

sample injection system
type: Class
subclass of: chromatography device
editor preferred term: sample injection system
has curation status: IAO_0000120
definition: An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
curator note: chromatography device

multiple wavelength detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: multiple wavelength detector
has curation status: IAO_0000120
definition: A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078

photoionization detector
type: Class
subclass of: gas chromatography detector
editor preferred term: photoionization detector
has curation status: IAO_0000120
definition: The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis.
term editor: PERSON:Daniel Schober
alternative label: PID
definition source: WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090

gas generator
type: Class
subclass of: gas chromatography equipment
editor preferred term: gas generator
has curation status: IAO_0000120
definition: An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
curator note: gas chromatography equipment

column jacket
type: Class
subclass of: chromatography device
editor preferred term: column jacket
has curation status: IAO_0000120
definition: A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
curator note: chromatography device

electron capture detector
type: Class
subclass of: gas chromatography detector
editor preferred term: electron capture detector
has curation status: IAO_0000120
definition: The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes.
term editor: PERSON:Daniel Schober
alternative label: ECD
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085

reversed phase column
type: Class
subclass of: chromatography column
editor preferred term: reversed phase column
has curation status: IAO_0000120
definition: A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106

injector lubricant
type: Class
subclass of: chromatography consumable
editor preferred term: injector lubricant
has curation status: IAO_0000120
definition: A lubricant used in liquid chromatography that eases sample injector penetration.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118

isolation of cell population
type: Class
subclass of: OBI_0600014
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred term: isolation of cell population
example of usage: removing CD4+ cells from PBMCs using magnetic beads.
has curation status: IAO_0000123
definition: a process in which a population of cells with certain characteristics is isolated from a larger population
term editor: Person: Bjoern Peters

DISCOVERY console
type: Class
subclass of: tecmag NMR console
editor preferred term: DISCOVERY console
has curation status: IAO_0000120
definition: The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
curator note: NMR instrument/NMR console

Bruker AMX series NMR instrument
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker AMX series NMR instrument
has curation status: IAO_0000120
definition: A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
curator note: NMR instrument

chromatofocusing column
type: Class
subclass of: chromatography column
editor preferred term: chromatofocusing column
has curation status: IAO_0000120
definition: A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209

NMR probe
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: part of
  some values from: NMR instrument
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: NMR probe
has curation status: IAO_0000120
definition: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014
curator note: NMR instrument

NMR magnet
type: Class
subclass of: device
editor preferred term: NMR magnet
has curation status: IAO_0000120
definition: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
curator note: NMR instrument

trap column
type: Class
subclass of: chromatography column
editor preferred term: trap column
has curation status: IAO_0000120
definition: A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261

flow probe
type: Class
subclass of: NMR probe
editor preferred term: flow probe
has curation status: IAO_0000120
definition: An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
curator note: NMR device

clinical chemistry assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: OBI_2000009
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_2000009
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: scattered molecular aggregate
  intersection of: Restriction
    on property: has specified input
    some values from: scattered molecular aggregate
editor preferred term: clinical chemistry assay
example of usage: Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters.
has curation status: IAO_0000120
definition: An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism.
term editor: Philippe Rocca-Serra
alternative label: chemical pathology
alternative label: detection of analyte in blood sample
definition source: url:https://en.wikipedia.org/wiki/Clinical_chemistry

flame ionization detector
type: Class
subclass of: gas chromatography detector
editor preferred term: flame ionization detector
has curation status: IAO_0000120
definition: A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample.
term editor: PERSON:Daniel Schober
alternative label: FID
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197

vial
type: Class
subclass of: container
editor preferred term: vial
has curation status: IAO_0000120
definition: A container made from solid material and primarily used for holding liquid.
term editor: https://orcid.org/0000-0002-8844-9165
definition source: https://en.wikipedia.org/wiki/Vial

magic angle spinning rotor
type: Class
subclass of: device
subclass of: Restriction
  on property: part of
  some values from: NMR instrument
editor preferred term: magic angle spinning rotor
has curation status: IAO_0000120
definition: A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle.
term editor: PERSON:Daniel Schober
alternative label: MAS rotor
definition source: WEB:<http://www.freepatentsonline.com/4352066.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
curator note: NMR instrument

Varian VXR spectrometer
type: Class
subclass of: Varian NMR instrument
editor preferred term: Varian VXR spectrometer
has curation status: IAO_0000120
definition: A Varian NMR spectrometer.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
curator note: NMR instrument

splitless GC injector
type: Class
subclass of: sample injection system
editor preferred term: splitless GC injector
has curation status: IAO_0000120
definition: Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060

preparative autosampler
type: Class
subclass of: liquid chromatography autosampler
editor preferred term: preparative autosampler
has curation status: IAO_0000120
definition: For preparative LC with injection of sample volumes ranging from L to mL ranges.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062

flow high resolution probe
type: Class
subclass of: Bruker high resolution probe
editor preferred term: flow high resolution probe
has curation status: IAO_0000120
definition: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
term editor: PERSON:Daniel Schober
alternative label: flow HR-probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
curator note: NMR probe

liquid chromatography valve
type: Class
subclass of: chromatography device
editor preferred term: liquid chromatography valve
has curation status: IAO_0000120
definition: A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
curator note: chromatography device

JEOL NMR probe
type: Class
subclass of: NMR probe
editor preferred term: JEOL NMR probe
has curation status: IAO_0000120
definition: An NMR probe that is manufactured by JEOL.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
curator note: NMR device

Bruker UltraShield Plus NMR magnet
type: Class
subclass of: Bruker NMR magnet
editor preferred term: Bruker UltraShield Plus NMR magnet
has curation status: IAO_0000120
definition: An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
curator note: NMR instrument

Bruker CryoProbe
type: Class
subclass of: Bruker NMR probe
editor preferred term: Bruker CryoProbe
has curation status: IAO_0000120
definition: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
curator note: NMR probe

column cartridge
type: Class
subclass of: chromatography device
editor preferred term: column cartridge
has curation status: IAO_0000120
definition: A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055

affinity column
type: Class
subclass of: chromatography column
editor preferred term: affinity column
has curation status: IAO_0000120
definition: An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094

tecmag NMR instrument
type: Class
subclass of: NMR instrument
editor preferred term: tecmag NMR instrument
has curation status: IAO_0000120
definition: An NMR instrument that is manufactured by tecmag.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
curator note: NMR instrument

gel filtration column
type: Class
subclass of: size exclusion column
editor preferred term: gel filtration column
has curation status: IAO_0000120
definition: A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104

fraction collector
type: Class
subclass of: chromatography instrument
editor preferred term: fraction collector
has curation status: IAO_0000120
definition: A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073

copy number variation profiling assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: genetic characteristics information
editor preferred term: copy number variation profiling assay
example of usage: Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796
has curation status: IAO_0000120
definition: An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping
term editor: Philippe Rocca-Serra
alternative label: CNV analysis

in-line filter
type: Class
subclass of: chromatography detector filter
editor preferred term: in-line filter
has curation status: IAO_0000120
definition: A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.appliedporous.com/frits-chromatography.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123

imaging NMR probe
type: Class
subclass of: NMR probe
editor preferred term: imaging NMR probe
has curation status: IAO_0000120
definition: An NMR probe that is designed for generating pictures from sample states via NMR imaging.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
curator note: NMR device

isolation of adherent cells
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
editor preferred term: isolation of adherent cells
has curation status: IAO_0000123
definition: 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.

Bruker AC series NMR instrument
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker AC series NMR instrument
has curation status: IAO_0000120
definition: A series of older Bruker NMR magnets, now out of production.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
curator note: NMR instrument

gas chromatography equipment
type: Class
subclass of: chromatography device
editor preferred term: gas chromatography equipment
has curation status: IAO_0000120
definition: Any device used in a gas chromatography experiment.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
curator note: will become defined class/xps

syringe filter
type: Class
subclass of: chromatography detector filter
editor preferred term: syringe filter
has curation status: IAO_0000120
definition: A small membrane filter of defined pore size, that filters samples from a syringe.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122

Bruker SampleRail system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: Bruker SampleRail system
has curation status: IAO_0000120
definition: This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207
curator note: NMR instrument

column compartment
type: Class
subclass of: chromatography device
editor preferred term: column compartment
has curation status: IAO_0000120
definition: For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068

capillary pump system
type: Class
subclass of: chromatography pump system
editor preferred term: capillary pump system
has curation status: IAO_0000120
definition: A pump system optimized for capillary chromatography.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051

evaporative light scattering detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: evaporative light scattering detector
has curation status: IAO_0000120
definition: The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082

isolation of PBMCs
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has specified input
  some values from: UBERON_0000178
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred term: isolation of PBMCs
example of usage: 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.
has curation status: IAO_0000120
definition: a process in which cells with a single nucleus are isolated from a blood sample
term editor: PERSON: bjoern peters
definition source: wiki http://en.wikipedia.org/wiki/PBMC

column cartridger
type: Class
subclass of: chromatography instrument
editor preferred term: column cartridger
has curation status: IAO_0000120
definition: A chromatography device where the column cartridge is inserted into and stabilised.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054

nitrogen generator
type: Class
subclass of: gas generator
editor preferred term: nitrogen generator
has curation status: IAO_0000120
definition: A gas generator that generates nitrogen gas.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034

needle assembly
type: Class
subclass of: chromatography device
editor preferred term: needle assembly
has curation status: IAO_0000120
definition: The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065

reverse transcribed polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: polymerase chain reaction
    intersection of: Restriction
      on property: immediately preceded by
      some values from: OBI_0600028
subclass of: Restriction
  on property: has specified input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: PCR product
editor preferred term: reverse transcribed polymerase chain reaction
example of usage: Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
has curation status: IAO_0000123
definition: 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.
editor note: 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
term editor: Philippe Rocca-Serra
alternative label: RT-PCR
alternative label: reverse transcription polymerase chain reaction

Bruker Capillary LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker Capillary LC-NMR platform
has curation status: IAO_0000120
definition: Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
curator note: NMR instrument
curator note: hyphenated NMR instrument platform

gas chromatography oven
type: Class
subclass of: gas chromatography equipment
editor preferred term: gas chromatography oven
has curation status: IAO_0000120
definition: A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
curator note: gas chromatography equipment

autosampler
type: Class
subclass of: device
editor preferred term: autosampler
has curation status: IAO_0000120
definition: An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
curator note: NMR instrument

isocratic pump system
type: Class
subclass of: chromatography pump system
editor preferred term: isocratic pump system
has curation status: IAO_0000120
definition: A pump system optimized for isocratic chromatography.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049

flash pump system
type: Class
subclass of: chromatography pump system
editor preferred term: flash pump system
has curation status: IAO_0000120
definition: Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048

Varian UNITY INOVA spectrometer
type: Class
subclass of: Varian NMR instrument
editor preferred term: Varian UNITY INOVA spectrometer
has curation status: IAO_0000120
definition: The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
curator note: NMR instrument

liquid NMR probe
type: Class
subclass of: NMR probe
editor preferred term: liquid NMR probe
has curation status: IAO_0000120
definition: An NMR probe that is designed to hold a liquid sample.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
curator note: NMR device

ion exchange column
type: Class
subclass of: chromatography column
editor preferred term: ion exchange column
has curation status: IAO_0000120
definition: An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105

Bruker NMR probe
type: Class
subclass of: NMR probe
editor preferred term: Bruker NMR probe
has curation status: IAO_0000120
definition: An NMR probe that is manufactured by Bruker.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231
curator note: NMR device, TODO: May need no definition.

anion trap column
type: Class
subclass of: trap column
editor preferred term: anion trap column
has curation status: IAO_0000120
definition: An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277

fluorescene detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: fluorescene detector
has curation status: IAO_0000120
definition: A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080

tecmag EAGLE probe
type: Class
subclass of: solid NMR probe
editor preferred term: tecmag EAGLE probe
has curation status: IAO_0000120
definition: The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
curator note: NMR probe

electrical conductivity detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: electrical conductivity detector
has curation status: IAO_0000120
definition: The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239

NMR instrument
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: NMR instrument
has curation status: IAO_0000120
definition: An Instrument which is used to carry out a NMR analysis of some sample.
term editor: PERSON:Daniel Schober
alternative label: MRI scanner
alternative label: NMR instrument
alternative label: magnetic resonance imaging scanner
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059
curator note: NMR instrument

Bruker UltraShield NMR magnet
type: Class
subclass of: Bruker NMR magnet
editor preferred term: Bruker UltraShield NMR magnet
has curation status: IAO_0000120
definition: An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design.
term editor: PERSON:Daniel Schober
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
curator note: NMR instrument

piston-seal
type: Class
subclass of: chromatography consumable
editor preferred term: piston-seal
has curation status: IAO_0000120
definition: The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116

mass selective detector
type: Class
subclass of: gas chromatography detector
editor preferred term: mass selective detector
has curation status: IAO_0000120
definition: A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier.
term editor: PERSON:Daniel Schober
alternative label: mass spectrometry detector
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198

spin column
type: Class
subclass of: chromatography column
editor preferred term: spin column
has curation status: IAO_0000120
definition: A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred term: manufacturer role
example of usage: 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.
has curation status: IAO_0000123
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI

transfer line
type: Class
subclass of: chromatography device
editor preferred term: transfer line
has curation status: IAO_0000120
definition: A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.freepatentsonline.com/5702671.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
curator note: chromatography device

gradient pump system
type: Class
subclass of: chromatography pump system
editor preferred term: gradient pump system
has curation status: IAO_0000120
definition: A pump system optimized for gradient chromatography.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050

high temperature column
type: Class
subclass of: chromatography column
editor preferred term: high temperature column
has curation status: IAO_0000120
definition: A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233

Bruker Ultrastabilized NMR magnet
type: Class
subclass of: Bruker NMR magnet
editor preferred term: Bruker Ultrastabilized NMR magnet
has curation status: IAO_0000120
definition: An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized.
term editor: PERSON:Daniel Schober
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
curator note: NMR instrument

scattered molecular aggregate
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has grain
  some values from: molecular entity
subclass of: Restriction
  on property: has grain
  all values from: molecular entity
editor preferred term: scattered molecular aggregate
example of usage: the sodium and chloride ions in a glass of salt water
has curation status: IAO_0000123
definition: a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
term editor: PERSON: Alan Ruttenberg
alternative label: Collective
definition source: 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

obsolete_molecular concentration
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_molecular concentration
example of usage: the phosphate concentration should be 0.1M
has curation status: IAO_0000123
definition: A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
term editor: PERSON: Alan Ruttenberg
definition source: Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
has obsolescence reason: IAO_0000228
deprecated: true

NMR sample tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: part of
  some values from: NMR instrument
editor preferred term: NMR sample tube
has curation status: IAO_0000120
definition: The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
curator note: NMR device

Varian UNITY spectrometer
type: Class
subclass of: Varian NMR instrument
editor preferred term: Varian UNITY spectrometer
has curation status: IAO_0000120
definition: The predecessor series of the Varian UNITY INOVA spectrometer.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
curator note: NMR instrument

AVANCE II spectrometer
type: Class
subclass of: Bruker NMR instrument
editor preferred term: AVANCE II spectrometer
has curation status: IAO_0000120
definition: A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
curator note: NMR instrument

y-column connector
type: Class
subclass of: column connector
editor preferred term: y-column connector
has curation status: IAO_0000120
definition: A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237

Bruker LC-NMR/MS platform
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker LC-NMR/MS platform
has curation status: IAO_0000120
definition: Includes the connection to a high-resolution TOF-LC-MS system.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
curator note: NMR instrument
curator note: hyphenated NMR instrument platform

refractive index detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: refractive index detector
has curation status: IAO_0000120
definition: For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081

anion exchange column
type: Class
subclass of: ion exchange column
editor preferred term: anion exchange column
has curation status: IAO_0000120
definition: An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095

plunger column
type: Class
subclass of: chromatography column
editor preferred term: plunger column
has curation status: IAO_0000120
definition: A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108

flame photometric detector
type: Class
subclass of: gas chromatography detector
editor preferred term: flame photometric detector
has curation status: IAO_0000120
definition: The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected.
term editor: PERSON:Daniel Schober
alternative label: FPD
definition source: WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091

chromatography pump system
type: Class
subclass of: chromatography instrument
editor preferred term: chromatography pump system
has curation status: IAO_0000120
definition: Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://en.wikipedia.org/wiki/Column_chromatography>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046

Bruker 1mm MicroProbe
type: Class
subclass of: Bruker NMR probe
editor preferred term: Bruker 1mm MicroProbe
has curation status: IAO_0000120
definition: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
curator note: NMR probe

Bruker BEST NMR system
type: Class
subclass of: Bruker autosampler
editor preferred term: Bruker BEST NMR system
has curation status: IAO_0000120
definition: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
term editor: PERSON:Daniel Schober
alternative label: Bruker Efficient Sample Transfer NMR
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
curator note: NMR instrument

chromatography detector filter
type: Class
subclass of: chromatography consumable
editor preferred term: chromatography detector filter
has curation status: IAO_0000120
definition: An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121

cation trap column
type: Class
subclass of: trap column
editor preferred term: cation trap column
has curation status: IAO_0000120
definition: A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278

column adapter
type: Class
subclass of: chromatography device
editor preferred term: column adapter
has curation status: IAO_0000120
definition: An Adapter that enabled the connection of a column to additional devices.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
curator note: chromatography device

pulsed amperometric detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: pulsed amperometric detector
has curation status: IAO_0000120
definition: A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC).
term editor: PERSON:Daniel Schober
alternative label: PAD
definition source: WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240

Bruker NMR instrument
type: Class
subclass of: NMR instrument
editor preferred term: Bruker NMR instrument
has curation status: IAO_0000120
definition: An NMR instrument that is manufactured by Bruker.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198
curator note: NMR instrument

Bruker NMR magnet
type: Class
subclass of: NMR magnet
editor preferred term: Bruker NMR magnet
has curation status: IAO_0000120
definition: An NMR magnet that is manufactured by Bruker.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186
curator note: NMR instrument

ozone-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
editor preferred term: ozone-induced chemiluminescence detector
has curation status: IAO_0000120
definition: Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088

tecmag NMR console
type: Class
subclass of: NMR console
editor preferred term: tecmag NMR console
has curation status: IAO_0000120
definition: An NMR console manufactured by tecmac.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
curator note: NMR instrument

JEOL NMR instrument
type: Class
subclass of: NMR instrument
editor preferred term: JEOL NMR instrument
has curation status: IAO_0000120
definition: An NMR instrument that is manufactured by JEOL.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226
curator note: NMR instrument

chromatography consumable
type: Class
subclass of: chromatography device
editor preferred term: chromatography consumable
has curation status: IAO_0000120
definition: A chromatography consumable is a consumable that is used in a chromatography experiment.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
curator note: chromatography device

column frit
type: Class
subclass of: chromatography device
editor preferred term: column frit
has curation status: IAO_0000120
definition: A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density).
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
curator note: chromatography device

liquid chromatography column
type: Class
subclass of: chromatography column
editor preferred term: liquid chromatography column
has curation status: IAO_0000120
definition: A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227

detector lamp
type: Class
subclass of: chromatography consumable
editor preferred term: detector lamp
has curation status: IAO_0000120
definition: A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119

chart recorder
type: Class
subclass of: chromatography device
editor preferred term: chart recorder
has curation status: IAO_0000120
definition: The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
curator note: chromatography device

open tubular column
type: Class
subclass of: chromatography column
editor preferred term: open tubular column
has curation status: IAO_0000120
definition: An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
term editor: PERSON:Daniel Schober
definition source: WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219

high resolution magic angle spin probe
type: Class
subclass of: Bruker high resolution probe
editor preferred term: high resolution magic angle spin probe
has curation status: IAO_0000120
definition: Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
term editor: PERSON:Daniel Schober
alternative label: high resolution MAS, hr-MAS
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
curator note: NMR probe

hydrogen generator
type: Class
subclass of: gas generator
editor preferred term: hydrogen generator
has curation status: IAO_0000120
definition: A gas generator that generates hydrogen gas.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035

glass column
type: Class
subclass of: chromatography column
editor preferred term: glass column
has curation status: IAO_0000120
definition: A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101

auto injector
type: Class
subclass of: sample injection system
editor preferred term: auto injector
has curation status: IAO_0000120
definition: A gas chromatography device that can auto-inject a small number of samples an inlet.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058

Varian NMR instrument
type: Class
subclass of: NMR instrument
editor preferred term: Varian NMR instrument
has curation status: IAO_0000120
definition: An NMR instrument that is manufactured by Varian.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234
curator note: NMR instrument

Bruker MATCH tube holder system
type: Class
subclass of: NMR sample holder
editor preferred term: Bruker MATCH tube holder system
has curation status: IAO_0000120
definition: The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube.
term editor: PERSON:Daniel Schober
alternative label: Bruker Multiple Adjustable Tube Clamp Holder
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
curator note: NMR instrument

Bruker SPE-NMR platform
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker SPE-NMR platform
has curation status: IAO_0000120
definition: A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
curator note: NMR instrument
curator note: hyphenated NMR instrument platform

guard column
type: Class
subclass of: chromatography device
editor preferred term: guard column
has curation status: IAO_0000120
definition: Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
curator note: chromatography device

protein expression profiling assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Class
        intersection of: OBI_0100051
        intersection of: Restriction
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
editor preferred term: protein expression profiling assay
example of usage: Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203
has curation status: IAO_0000120
definition: An assay that determines protein expression and translation activity using protein extracts collected from a material entity.
term editor: Phlippe Rocca-Serra
alternative label: proteomic analysis
definition source: OBI branch derived

high resolution probe with automatic tuning and matching
type: Class
subclass of: Bruker high resolution probe
editor preferred term: high resolution probe with automatic tuning and matching
has curation status: IAO_0000120
definition: The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
term editor: PERSON:Daniel Schober
alternative label: High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
curator note: NMR probe

fluorine-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
editor preferred term: fluorine-induced chemiluminescence detector
has curation status: IAO_0000120
definition: A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087

size exclusion column
type: Class
subclass of: chromatography column
editor preferred term: size exclusion column
has curation status: IAO_0000120
definition: A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100

chromatography splitter
type: Class
subclass of: chromatography device
editor preferred term: chromatography splitter
has curation status: IAO_0000120
definition: An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
curator note: chromatography device

Bruker micro imaging probe
type: Class
subclass of: Bruker NMR probe
editor preferred term: Bruker micro imaging probe
has curation status: IAO_0000120
definition: For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
curator note: NMR probe

custom made column
type: Class
subclass of: chromatography column
editor preferred term: custom made column
has curation status: IAO_0000120
definition: A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234

gel permeation column
type: Class
subclass of: chromatography column
editor preferred term: gel permeation column
has curation status: IAO_0000120
definition: A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103

NMR spectroscopy assay
type: Class
subclass of: assay
editor preferred term: NMR spectroscopy assay
example of usage: Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
has curation status: IAO_0000123
definition: An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
term editor: Philippe Rocca-Serra
alternative label: Nuclear magnetic resonance spectroscopy
definition source: url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy

Bruker SampleJet system
type: Class
subclass of: Bruker autosampler
editor preferred term: Bruker SampleJet system
has curation status: IAO_0000120
definition: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
curator note: NMR instrument

JEOL ECX NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
editor preferred term: JEOL ECX NMR spectrometer
has curation status: IAO_0000120
definition: The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
curator note: NMR instrument

DNA sequencing assay
type: Class
equivalent class: Class
  intersection of: OBI_0600047
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400103
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: DNA extract
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001573
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: primary structure of DNA macromolecule
subclass of: OBI_0600047
editor preferred term: DNA sequencing assay
example of usage: Illumina (Solexa) sequencing is an example of DNA sequencing
has curation status: IAO_0000123
definition: A sequencing assay which determines information on the sequence of a DNA molecule.
term editor: Philippe Rocca-Serra
alternative label: nucleotide sequencing
definition source: url:https://en.wikipedia.org/wiki/DNA_sequencing

quaternary pump system
type: Class
subclass of: chromatography pump system
editor preferred term: quaternary pump system
has curation status: IAO_0000120
definition: A pump system that pump and mix up to four different solvents in parallel.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047

carbon nanotube column
type: Class
subclass of: chromatography column
editor preferred term: carbon nanotube column
has curation status: IAO_0000120
definition: Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107

Bruker solid magic angle spinning probe
type: Class
subclass of: Bruker NMR probe
editor preferred term: Bruker solid magic angle spinning probe
has curation status: IAO_0000120
definition: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei.
term editor: PERSON:Daniel Schober
alternative label: solid MAS probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
curator note: NMR probe

hematology assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: hemopoiesis
editor preferred term: hematology assay
example of usage: Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943
has curation status: IAO_0000123
definition: An assay that studies blood and blood producing organs using a variety of techniques and instruments
term editor: Philippe Rocca-Serra
alternative label: blood analysis
alternative label: haematology
definition source: OBI branch derived

Varian MERCURY spectrometer
type: Class
subclass of: Varian NMR instrument
editor preferred term: Varian MERCURY spectrometer
has curation status: IAO_0000120
definition: MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation.
term editor: PERSON:Daniel Schober
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
curator note: NMR instrument

Bruker Metabolic Profiler
type: Class
subclass of: Bruker NMR instrument
editor preferred term: Bruker Metabolic Profiler
has curation status: IAO_0000120
definition: An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
curator note: NMR instrument
curator note: hyphenated NMR instrument platform

column heater
type: Class
subclass of: chromatography instrument
editor preferred term: column heater
has curation status: IAO_0000120
definition: The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040

DNA methylation profiling assay
type: Class
subclass of: OBI_0002020
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: deoxyribonucleotide
      intersection of: Restriction
        on property: has part
        some values from: methyl group
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: data item
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
editor preferred term: DNA methylation profiling assay
example of usage: Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979
has curation status: IAO_0000122
definition: An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
term editor: Philippe Rocca-Serra
alternative label: DNA methylation profiling
definition source: OBI branch derived

JEOL CapNMR probe
type: Class
subclass of: JEOL NMR probe
editor preferred term: JEOL CapNMR probe
has curation status: IAO_0000120
definition: The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
curator note: NMR probe

acquisition computer
type: Class
subclass of: OBI_0400107
subclass of: Restriction
  on property: has function
  some values from: information processor function
editor preferred term: acquisition computer
has curation status: IAO_0000120
definition: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
curator note: NMR instrument

gas chromatography detector
type: Class
subclass of: chromatography detector
editor preferred term: gas chromatography detector
has curation status: IAO_0000120
definition: A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors.
term editor: PERSON:Daniel Schober
alternative label: FID
definition source: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
curator note: chromatography detector, defined class/xps

gas purifier
type: Class
subclass of: gas chromatography equipment
editor preferred term: gas purifier
has curation status: IAO_0000120
definition: Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
curator note: gas chromatography equipment

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred term: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000122
definition: is an objective to transform a material entity into spatially separated components.
term editor: PPPB branch
definition source: PPPB branch

indirect detection probe
type: Class
subclass of: NMR probe
editor preferred term: indirect detection probe
has curation status: IAO_0000120
definition: An NMR probe designed to allow the indirect detection of acquisition nuclei.
term editor: PERSON:Daniel Schober
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
curator note: NMR device

JEOL ECA NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
editor preferred term: JEOL ECA NMR spectrometer
has curation status: IAO_0000120
definition: The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
curator note: NMR instrument

atomic emission detector
type: Class
subclass of: gas chromatography detector
editor preferred term: atomic emission detector
has curation status: IAO_0000120
definition: Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element.
term editor: PERSON:Daniel Schober
alternative label: AED
definition source: WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086

clustered data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200175
subclass of: data set
editor preferred term: clustered data set
example of usage: A clustered data set is the output of a K means clustering data transformation
has curation status: IAO_0000125
definition: A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: data set with assigned discovered class labels
curator note: AR thinks could be a data item instead

data set of features
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200184
subclass of: data set
editor preferred term: data set of features
has curation status: IAO_0000125
definition: A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee

differential expression analysis data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200031
subclass of: OBI_0200000
editor preferred term: differential expression analysis data transformation
has curation status: IAO_0000122
definition: A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals.
term editor: Dan Berrios
term editor: James Malone
term editor: Melanie Courtot
term editor: Monnie McGee
definition source: WEB:

urine specimen
type: Class
equivalent class: Class
  intersection of: OBI_2000009
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: UBERON_0001088
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600005
subclass of: OBI_2000009
editor preferred term: urine specimen
has curation status: IAO_0000120
definition: a portion of urine collected from an organism
editor note: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
editor note: 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
editor note: are we happy calling collection of urine a material separation?

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: material entity
editor preferred term: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
has curation status: IAO_0000122
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
term editor: bp
definition source: bp

fuzzy clustering objective
type: Class
subclass of: OBI_0200166
editor preferred term: fuzzy clustering objective
has curation status: IAO_0000122
definition: A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
term editor: James Malone
definition source: PERSON: James Malone
definition source: PERSON: Ryan Brinkman

device setting
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: processed material
editor preferred term: device setting
example of usage: 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
has curation status: IAO_0000123
definition: a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
editor note: 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
term editor: PERSON: Frank Gibson

blood specimen
type: Class
equivalent class: Class
  intersection of: OBI_2000009
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: UBERON_0000178
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600005
subclass of: OBI_2000009
editor preferred term: blood specimen
example of usage: blood drawn from a human for glucose assay
has curation status: IAO_0000122
definition: a material entity derived from a portion of blood collected from an organism
term editor: Bjoern Peters
definition source: Bjoern Peters

data set of predicted values according to fitted curve
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200072
subclass of: data set
editor preferred term: data set of predicted values according to fitted curve
has curation status: IAO_0000125
definition: A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee

data representational model
type: Class
subclass of: directive information entity
editor preferred term: data representational model
example of usage: The Cytoscape application is commonly used to visualize data representational models about biological entities. It can read and write several serializations of data representational models, including BioPAX.
example of usage: gene regulatory graph model
example of usage: phylogenetic tree
example of usage: protein interaction network
has curation status: IAO_0000120
definition: An information content entity representing the relationships between data items.
term editor: Melanie Courtot
alternative label: data structure
alternative label: data structure specification
definition source: GROUP: OBI
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100051
editor preferred term: specimen collection process
example of usage: 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, collecting a stone from a site
has curation status: IAO_0000122
definition: A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
editor note: Definition updated following discussion on 2024-10-07 OBI dev call.
editor note: 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.
editor note: 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.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative label: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop

background corrected data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: background correction data transformation
subclass of: data set
editor preferred term: background corrected data set
has curation status: IAO_0000125
definition: A data set that is produced as the output of a background correction data transformation.
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot

enzyme-linked immunosorbent assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: immunoglobulin complex, circulating
  intersection of: Restriction
    on property: has specified input
    some values from: immunoglobulin complex, circulating
editor preferred term: enzyme-linked immunosorbent assay
example of usage: 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
has curation status: IAO_0000120
definition: An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
term editor: IEDB
alternative label: ELISA
definition source: IEDB

error corrected data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: error correction data transformation
subclass of: data set
editor preferred term: error corrected data set
has curation status: IAO_0000125
definition: A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee

class prediction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has specified output
    some values from: classified data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200179
subclass of: OBI_0200000
editor preferred term: class prediction data transformation
has curation status: IAO_0000122
definition: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
term editor: James Malone
alternative label: supervised classification data transformation
definition source: PERSON: James Malone

BrdU incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: characteristic of
        some values from: 5-bromo-2'-deoxyuridine
  intersection of: Restriction
    on property: has specified input
    some values from: 5-bromo-2'-deoxyuridine
editor preferred term: BrdU incorporation assay
example of usage: The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU.
has curation status: IAO_0000120
definition: A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies.
term editor: IEDB
definition source: IEDB

obsolete intracellular cytokine staining assay
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete intracellular cytokine staining assay
example of usage: Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
has curation status: IAO_0000120
definition: The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
term editor: IEDB
alternative label: ICCS
alternative label: ICS
definition source: IEDB
has obsolescence reason: IAO_0000227
term replaced by: flow cytometry assay
IEDB alternative term: intracellular cytokine staining (ICS)
deprecated: true

background correction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has specified output
    some values from: background corrected data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200173
subclass of: OBI_0200000
editor preferred term: background correction data transformation
has curation status: IAO_0000122
definition: A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
term editor: James Malone
definition source: PERSON: James Malone

obsolete MHC multimer staining assay
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete MHC multimer staining assay
example of usage: Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
has curation status: IAO_0000120
definition: An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
term editor: IEDB
alternative label: MHC tetramer assay
definition source: IEDB
has obsolescence reason: IAO_0000227
term replaced by: OBI_1110179
IEDB alternative term: MHC tetramer/multimer staining
deprecated: true

error correction data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200186
subclass of: OBI_0200000
editor preferred term: error correction data transformation
has curation status: IAO_0000122
definition: An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
term editor: James Malone
term editor: Monnie McGee
definition source: EDITORS

tritiated thymidine incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: characteristic of
        some values from: tritiated thymidine
  intersection of: Restriction
    on property: has specified input
    some values from: tritiated thymidine
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: radioactivity detection
    intersection of: OBI_0003368
editor preferred term: tritiated thymidine incorporation assay
example of usage: The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
has curation status: IAO_0000120
definition: A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
term editor: IEDB
definition source: IEDB

sample from organism
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
editor preferred term: sample from organism
has curation status: IAO_0000002
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: 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.

statistical hypothesis test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: OBI_0200000
editor preferred term: statistical hypothesis test
has curation status: IAO_0000120
definition: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
term editor: James Malone
definition source: PERSON: James Malone

center value
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200181
subclass of: data item
editor preferred term: center value
has curation status: IAO_0000125
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: median

statistical hypothesis test objective
type: Class
subclass of: OBI_0200166
editor preferred term: statistical hypothesis test objective
has curation status: IAO_0000123
definition: 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.
term editor: James Malone
term editor: Person:Helen Parkinson
alternative label: hypothesis test objective
definition source: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing

reduced dimension data set
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200182
subclass of: data set
editor preferred term: reduced dimension data set
has curation status: IAO_0000125
definition: A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
editor preferred term: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: IAO_0000123
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.

average value
type: Class
equivalent class: Restriction
  on property: is specified output of
  some values from: OBI_0200170
subclass of: data item
editor preferred term: average value
has curation status: IAO_0000125
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: arithmetic mean

whole organism preparation
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: derives from
  some values from: OBI_0100026
editor preferred term: whole organism preparation
example of usage: putting a mouse in the blender. Not: putting a mouse on a scale
has curation status: IAO_0000123
definition: 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
editor note: 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.

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred term: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000120
definition: 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).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives

obsolete_study result
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_study result
has curation status: IAO_0000120
definition: Study result is an information content entity that is a specified data output of a study.
definition source: GROUP: OBI
has obsolescence reason: IAO_0000230
deprecated: true

specimen collection objective
type: Class
subclass of: objective specification
editor preferred term: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: IAO_0000122
definition: A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
editor note: OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
term editor: Bjoern Peters
definition source: Bjoern Peters

creating a mixture of molecules in solution
type: Class
subclass of: material combination
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0302729
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
editor preferred term: creating a mixture of molecules in solution
example of usage: The production of PBS
has curation status: IAO_0000120
definition: is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
term editor: Bjoern Peters
definition source: PERSON: Helen Parkinson

material combination objective
type: Class
subclass of: material transformation objective
editor preferred term: material combination objective
has curation status: IAO_0000122
definition: is an objective to obtain an output material that contains several input materials.
term editor: PPPB branch
definition source: bp

nucleotide overhang cloning
type: Class
subclass of: OBI_0600064
editor preferred term: nucleotide overhang cloning
example of usage: Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
has curation status: IAO_0000120
definition: Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
term editor: Helen Parkinson

rodent care protocol
type: Class
subclass of: animal care protocol
editor preferred term: rodent care protocol
example of usage: Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
has curation status: IAO_0000123
definition: A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
term editor: Bjoern Peters
definition source: Bjoern Peters

454 Genome Sequence 20
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
editor preferred term: 454 Genome Sequence 20
example of usage: PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
has curation status: IAO_0000120
definition: is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
term editor: Philippe Rocca-Serra
alternative label: GS 20

immunoprecipitation
type: Class
subclass of: OBI_0600014
subclass of: Restriction
  on property: has specified input
  some values from: immunoglobulin complex, circulating
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
editor preferred term: immunoprecipitation
example of usage: PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
has curation status: IAO_0000123
definition: is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
term editor: Philippe Rocca-Serra
definition source: OBI plan and planned process branch

ABI 377 automated sequencer
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000776
editor preferred term: ABI 377 automated sequencer
has curation status: IAO_0000120
definition: is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
term editor: Philippe Rocca-Serra
definition source: Applied Biosystems

recombination enzyme based cloning
type: Class
subclass of: OBI_0600064
editor preferred term: recombination enzyme based cloning
has curation status: IAO_0000123
definition: 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

MeDIP-seq assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: OBI_0001954
subclass of: OBI_0600047
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: Restriction
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: chromatin
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: deoxyribonucleotide
      intersection of: Restriction
        on property: has part
        some values from: methyl group
subclass of: Restriction
  on property: has part
  some values from: chromatin immunoprecipitation
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_0600047
subclass of: Restriction
  on property: has specified input
  some values from: DNA extract
subclass of: Restriction
  on property: has specified output
  some values from: sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
editor preferred term: MeDIP-seq assay
example of usage: PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
has curation status: IAO_0000120
definition: A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
term editor: Philippe Rocca-Serra
alternative label: Methylated DNA immunoprecipitation sequencing assay
definition source: url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation

animal feeding
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: feed role
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100026
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0100026
editor preferred term: animal feeding
example of usage: giving crickets to a snake.
has curation status: IAO_0000123
definition: animal feeding is a process in which animals are provided with food
editor note: In an investigation, this will typically be part of an animal care process
term editor: Bjoern Peters
definition source: branch derived

chain termination sequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      union of: ABI 377 automated sequencer
      union of: Li-Cor 4300 DNA Analysis System
subclass of: Restriction
  on property: has specified input
  some values from: PCR product
editor preferred term: chain termination sequencing assay
example of usage: PMID: 271968. DNA sequencing with chain-terminating inhibitors.
has curation status: IAO_0000120
definition: A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
term editor: Philippe Rocca-Serra
alternative label: Sanger sequencing
alternative label: dye terminator sequencing
definition source: url:https://en.wikipedia.org/wiki/Sanger_sequencing

AB SOLiD System
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000776
editor preferred term: AB SOLiD System
example of usage: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
has curation status: IAO_0000120
definition: is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
term editor: Philippe Rocca-Serra
definition source: Applied Biosystems

Helicos sequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: HeliScope Single Molecule Sequencer
  intersection of: Restriction
    on property: has specified input
    some values from: HeliScope Single Molecule Sequencer
editor preferred term: Helicos sequencing assay
example of usage: PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
has curation status: IAO_0000120
definition: A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length.
term editor: Philippe Rocca-Serra
alternative label: true single molecule sequencing
definition source: url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing

obsolete_DNA ligase
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_DNA ligase
has curation status: IAO_0000123
definition: A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
term editor: Kevin Clancy, Bjoern Peters
alternative label: ligase
has obsolescence reason: IAO_0000228
deprecated: true

survival assessment assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100026
subclass of: Restriction
  on property: has specified output
  some values from: survival rate
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: OBI_0100026
editor preferred term: survival assessment assay
has curation status: IAO_0000123
definition: An assay that measures the occurrence of death events in one or more organisms over time

support vector machine
type: Class
subclass of: class prediction data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200179
editor preferred term: support vector machine
has curation status: IAO_0000123
definition: 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.
term editor: James Malone
term editor: Ryan Brinkman
alternative label: SVM
definition source: PERSON: Ryan Brinkman

self-organizing map
type: Class
subclass of: OBI_0200175
subclass of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      union of: clustered data set
      union of: topologically preserved clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200178
editor preferred term: self-organizing map
has curation status: IAO_0000125
definition: 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.
term editor: James Malone
term editor: Ryan Brinkman
alternative label: SOM
definition source: PERSON: Ryan Brinkman

454 Genome Sequencer FLX
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
editor preferred term: 454 Genome Sequencer FLX
example of usage: PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10.
has curation status: IAO_0000120
definition: is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.
term editor: Philippe Rocca-Serra
alternative label: 454 GS FLX
alternative label: GS-FLX
definition source: adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay

Illumina Genome Analyzer II
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000759
editor preferred term: Illumina Genome Analyzer II
example of usage: PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
has curation status: IAO_0000120
definition: is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
term editor: Philippe Rocca-Serra
definition source: Illumina Corporation

decision tree induction objective
type: Class
subclass of: OBI_0200166
editor preferred term: decision tree induction objective
has curation status: IAO_0000123
definition: 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.
term editor: James Malone

Edman degradation
type: Class
subclass of: OBI_0600047
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: characteristic of
        some values from: material entity
  intersection of: Restriction
    on property: has specified input
    some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: information content entity
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: SO_0000104
editor preferred term: Edman degradation
example of usage: Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT.
has curation status: IAO_0000120
definition: A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis.
term editor: IEDB
definition source: IEDB

SOLiD sequencing assay
type: Class
subclass of: DNA sequencing by ligation assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: AB SOLiD System
  intersection of: Restriction
    on property: has specified input
    some values from: AB SOLiD System
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
    union of: PR_000023089
editor preferred term: SOLiD sequencing assay
example of usage: PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
has curation status: IAO_0000120
definition: A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles.
term editor: Philippe Rocca-Serra
definition source: url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing

decision tree building data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
subclass of: OBI_0200000
editor preferred term: decision tree building data transformation
has curation status: IAO_0000120
definition: A decision tree building data transformation is a data transformation that has objective decision tree induction.
term editor: James Malone
definition source: PERSON: James Malone

laboratory animal care
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: animal care protocol
subclass of: planned process
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: OBI_0100026
    intersection of: Restriction
      on property: located in
      some values from: site
editor preferred term: laboratory animal care
has curation status: IAO_0000123
definition: a process that realizes an animal care protocol that specifies how animals are kept and maintained

yeast artificial chromosome vector
type: Class
subclass of: double-stranded DNA
subclass of: cloning vector
subclass of: Restriction
  on property: has role
  some values from: cloning vector role
editor preferred term: yeast artificial chromosome vector
has curation status: IAO_0000123
definition: 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
editor note: this should be a child of 'chromosome' if we import that from another source
term editor: Kevin Clancy, Bjoern Peters
alternative label: YAC

Li-Cor 4300 DNA Analysis System
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000769
editor preferred term: Li-Cor 4300 DNA Analysis System
has curation status: IAO_0000120
definition: is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
term editor: Philippe Rocca-Serra
definition source: OBI and Li-Cor

library preparation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: double-stranded DNA
subclass of: Restriction
  on property: has specified output
  some values from: Class
    union of: clonal cDNA library
    union of: paired-end library
    union of: single fragment library
    union of: OBI_1000029
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: library preparation
example of usage: 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.
has curation status: IAO_0000120
definition: 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.
term editor: Philippe Rocca-Serra
alternative label: library construction

pathogen challenge
type: Class
subclass of: OBI_0003456
subclass of: Restriction
  on property: realizes
  some values from: host role
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: role of
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: role of
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
editor preferred term: pathogen challenge
has curation status: IAO_0000123
definition: The administration of a live pathogenic organism to a host.

GenePattern software
type: Class
subclass of: software
editor preferred term: GenePattern software
has curation status: IAO_0000120
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
term editor: James Malone
term editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/

graph of vertices
type: Class
subclass of: graph
editor preferred term: graph of vertices
example of usage: For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
has curation status: IAO_0000123
definition: 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.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term editor: James Malone
definition source: WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html

animal care protocol
type: Class
subclass of: protocol
editor preferred term: animal care protocol
example of usage: Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
has curation status: IAO_0000123
definition: An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
term editor: Bjoern Peters
definition source: Bjoern Peters

ChIP-seq assay
type: Class
equivalent class: Class
  intersection of: OBI_0001954
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400103
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: DNA sequencing assay
      intersection of: OBI_0003368
subclass of: OBI_0001954
editor preferred term: ChIP-seq assay
example of usage: PMID: 19275939
has curation status: IAO_0000122
definition: An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin
term editor: Bjoern Peters
term editor: Philippe Rocca-Serra
alternative label: chromatin immunoprecipitation sequencing assay
definition source: url:https://en.wikipedia.org/wiki/ChIP-sequencing

HeliScope Single Molecule Sequencer
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000757
editor preferred term: HeliScope Single Molecule Sequencer
has curation status: IAO_0000120
definition: is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
term editor: Philippe Rocca-Serra

pathogen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: OBI_0100026
subclass of: Restriction
  on property: realized in
  all values from: OGMS_0000063
editor preferred term: pathogen role
example of usage: 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
has curation status: IAO_0000120
definition: 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
term editor: GROUP: Role Branch
definition source: OBI
curator note: 6 April 2009: from the Vaccine Community

vaccine production
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: vaccine preparation
example of usage: The production of B. pertussis vaccine.
has curation status: IAO_0000120
definition: A planned process with the objective to create a vaccine.
definition source: OBI

immunologic adjuvant role
type: Class
subclass of: OBI_1110092
subclass of: Restriction
  on property: realized in
  all values from: immune response
editor preferred term: immunologic adjuvant role
example of usage: 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
has curation status: IAO_0000120
definition: The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
editor note: 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'.
term editor: GROUP: Role branch
definition source: Vaccine Ontology, Wikipedia, OBI
curator note: Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891

glucose tolerance test
type: Class
subclass of: OBI_0003040
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100017
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has part
  some values from: OBI_0600007
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: measuring glucose concentration in blood serum assay
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: Insulin resistance
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: biological feature identification objective
editor preferred term: glucose tolerance test
example of usage: PMID: 19527607
has curation status: IAO_0000122
definition: An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
term editor: Philippe Rocca-Serra
definition source: NuGO OBI plan branch

paired-end library
type: Class
subclass of: processed material
editor preferred term: paired-end library
example of usage: 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.
has curation status: IAO_0000123
definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
term editor: Philippe Rocca-Serra
alternative label: mate-paired library
alternative label: paired-end tag (PET) library
definition source: adapted from information provided by Solid web site

DNA sequencing by ligation assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has specified input
  some values from: PR_000023089
editor preferred term: DNA sequencing by ligation assay
example of usage: ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing).
has curation status: IAO_0000123
definition: A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase
term editor: Philippe Rocca-Serra
definition source: url:https://en.wikipedia.org/wiki/Sequencing_by_ligation

Solexa sequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: Illumina Genome Analyzer II
  intersection of: Restriction
    on property: has specified input
    some values from: Illumina Genome Analyzer II
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
editor preferred term: Solexa sequencing assay
example of usage: PMID: 18987734
has curation status: IAO_0000120
definition: A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
term editor: Philippe Rocca-Serra
alternative label: reversible terminator sequencing
definition source: Solexa web site (SS_DNAsequencing.pdf document available on july 2009)

host role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: OBI_0100026
editor preferred term: host role
example of usage: 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
has curation status: IAO_0000120
definition: 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
editor note: 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
term editor: GROUP: Role Branch
definition source: 30 Mar09 submitted by vaccine community
definition source: OBI
definition source: http://en.wikipedia.org/wiki/Host_(biology)

peak matching
type: Class
subclass of: OBI_0200000
editor preferred term: peak matching
has curation status: IAO_0000123
definition: 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
term editor: James Malone
term editor: Ryan Brinkman
definition source: PERSON: Ryan Brinkman

k-nearest neighbors
type: Class
subclass of: OBI_0200171
subclass of: OBI_0200175
subclass of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: OBI_0200178
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200172
editor preferred term: k-nearest neighbors
has curation status: IAO_0000125
definition: A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
term editor: James Malone
alternative label: k-NN
definition source: PERSON: James Malone

rodent care
type: Class
subclass of: laboratory animal care
subclass of: Restriction
  on property: has part
  some values from: animal feeding
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: contain function
    intersection of: Restriction
      on property: characteristic of
      some values from: OBI_0400171
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: rodent care protocol
subclass of: Restriction
  on property: has specified input
  some values from: Rodentia
subclass of: Restriction
  on property: has specified output
  some values from: Rodentia
editor preferred term: rodent care
example of usage: keeping animal
has curation status: IAO_0000123
definition: 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.
term editor: PPPB branch
definition source: PPPB branch

cloning plasmid
type: Class
equivalent class: Class
  intersection of: plasmid
  intersection of: Restriction
    on property: has role
    some values from: cloning vector role
subclass of: plasmid
subclass of: cloning vector
editor preferred term: cloning plasmid
has curation status: IAO_0000123
definition: 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.
editor note: Note: 'cloning vector role' is really a function. Should be dealt with globally

pyrosequencing assay
type: Class
subclass of: DNA sequencing by synthesis assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      union of: 454 Genome Sequence 20
      union of: 454 Genome Sequencer FLX
editor preferred term: pyrosequencing assay
example of usage: Pyrosequencing sheds light on DNA sequencing. PMID:1115661
has curation status: IAO_0000120
definition: A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
term editor: Philippe Rocca-Serra
definition source: url:http://en.wikipedia.org/wiki/Pyrosequencing

recombinant vector
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600064
subclass of: processed material
editor preferred term: recombinant vector
has curation status: IAO_0000123
definition: 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.

restriction enzyme
type: Class
subclass of: PR_000000001
subclass of: Restriction
  on property: participates in
  some values from: catalytic activity
editor preferred term: restriction enzyme
example of usage: The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
has curation status: IAO_0000123
definition: an enzyme that has a specific target cleavage sites within nucleic acids
term editor: Kevin Clancy, Bjoern Peters
curator note: 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments

DNA sequencing by synthesis assay
type: Class
subclass of: DNA sequencing assay
subclass of: Restriction
  on property: has specified input
  some values from: DNA polymerase complex
editor preferred term: DNA sequencing by synthesis assay
example of usage: Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing
has curation status: IAO_0000123
definition: A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
term editor: Philippe Rocca-Serra
definition source: url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html

NTP-2000
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: manufacturing
subclass of: Restriction
  on property: has role
  some values from: feed role
editor preferred term: NTP-2000
has curation status: IAO_0000123
definition: a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
term editor: Jennifer Fostel, Bjoern Peters

single fragment library
type: Class
subclass of: processed material
editor preferred term: single fragment library
has curation status: IAO_0000123
definition: is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
term editor: Philippe Rocca-Serra
alternative label: fragment library

cloning vector
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: cloning vector role
subclass of: nucleic acid
subclass of: processed material
subclass of: OBI_1110108
subclass of: Restriction
  on property: is specified output of
  some values from: material processing
editor preferred term: cloning vector
has curation status: IAO_0000123
definition: 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.

restriction enzyme based cloning
type: Class
subclass of: OBI_0600064
subclass of: Restriction
  on property: has part
  some values from: OBI_0302892
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: cloning vector role
    intersection of: Restriction
      on property: role of
      some values from: nucleic acid restriction enzyme digest
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: cloning insert role
    intersection of: Restriction
      on property: role of
      some values from: nucleic acid restriction enzyme digest
editor preferred term: restriction enzyme based cloning
has curation status: IAO_0000123
definition: 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.
term editor: Kevin Clancy, Bjoern Peters

Student's t-test
type: Class
subclass of: statistical hypothesis test
subclass of: Restriction
  on property: has specified output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
editor preferred term: Student's t-test
has curation status: IAO_0000123
definition: 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.
term editor: James Malone
definition source: WEB: http://en.wikipedia.org/wiki/T-test

material sample role
type: Class
subclass of: specimen role
editor preferred term: material sample role
example of usage: 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.
has curation status: IAO_0000125
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 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.
term tracker item: https://github.com/obi-ontology/obi/issues/1013

topologically preserved clustered data set
type: Class
subclass of: clustered data set
editor preferred term: topologically preserved clustered data set
example of usage: the output data set generated from a self-organizing map.
has curation status: IAO_0000125
definition: 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.
term editor: James Malone
definition source: PERSON: James Malone

nucleic acid restriction enzyme digest
type: Class
equivalent class: Class
  intersection of: nucleic acid
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600050
      intersection of: Restriction
        on property: has specified input
        some values from: nucleic acid
      intersection of: Restriction
        on property: has participant
        some values from: restriction enzyme
subclass of: nucleic acid
subclass of: processed material
editor preferred term: nucleic acid restriction enzyme digest
has curation status: IAO_0000123
definition: 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
term editor: Kevin Clancy, Bjoern Peters

immune response assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: immune response
editor preferred term: immune response assay
example of usage: Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA.
has curation status: IAO_0000123
definition: An assay that determines information about an immune response
term editor: Bjoern Peters
term editor: Randi Vita
definition source: IEDB

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection process
  intersection of: Restriction
    on property: has specified input
    some values from: material entity
  intersection of: Restriction
    on property: has specified output
    some values from: material sample
subclass of: specimen collection process
editor preferred term: material sampling process
has curation status: IAO_0000123
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
alternative label: sample collection
alternative label: sampling
term tracker item: https://github.com/obi-ontology/obi/issues/1002

material sample
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: OBI_0100051
editor preferred term: material sample
example of usage: 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.
has curation status: IAO_0000123
definition: A material entity that has the material sample role
term editor: OBI: workshop
alternative label: sample
alternative label: sample population
term tracker item: https://github.com/obi-ontology/obi/issues/1013

bisulfite sequencing assay
type: Class
subclass of: DNA sequencing assay
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: deoxyribonucleotide
      intersection of: Restriction
        on property: has part
        some values from: methyl group
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: DNA sequencing assay
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified input
  some values from: DNA extract
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: measurement datum
    intersection of: OBI_0001573
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
editor preferred term: bisulfite sequencing assay
example of usage: PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J.
has curation status: IAO_0000120
definition: A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
term editor: Philippe Rocca-Serra
term editor: Sagar Jain
definition source: url:https://en.wikipedia.org/wiki/Bisulfite_sequencing

CART
type: Class
subclass of: decision tree building data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
editor preferred term: CART
has curation status: IAO_0000122
definition: A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
term editor: James Malone
alternative label: classification and regression trees
definition source: BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.

study design independent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: OBI_0500000
editor preferred term: independent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
has curation status: IAO_0000122
definition: a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
editor note: 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative label: experimental factor
alternative label: independent variable
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
ISA alternative term: study factor

study design dependent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: OBI_0500000
editor preferred term: dependent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
has curation status: IAO_0000122
definition: dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
editor note: 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative label: dependent variable
definition source: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.

anticoagulant-containing test tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: surrounded by
  some values from: Restriction
    on property: has part
    some values from: Restriction
      on property: has grain
      some values from: sodium citrate dihydrate
editor preferred term: anticoagulant-containing test tube
has curation status: IAO_0000120
definition: A 'blue top' test tube that contains anticoagulant for storing blood specimens'
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

study design controlled variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: OBI_0500000
editor preferred term: controlled variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable.
has curation status: IAO_0000122
definition: Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent.
editor note: 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative label: controlled variable
definition source: WEB: http://en.wikipedia.org/wiki/Control_variable
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.

human antithrombin-III in blood assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: scattered molecular aggregate
      intersection of: Restriction
        on property: has grain
        some values from: PR_000003252
subclass of: Restriction
  on property: has specified output
  some values from: scalar measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: blood coagulation
editor preferred term: human antithrombin-III in blood assay
example of usage: PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
has curation status: IAO_0000122
definition: An assay that measures the amount of antithrombin III in blood.
term editor: Alan Ruttenberg
alternative label: AT-III assay
definition source: url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06

fluorescently labeled MHC multimer
type: Class
subclass of: OBI_0001936
subclass of: Restriction
  on property: has part
  some values from: OBI_0002744
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600038
subclass of: Restriction
  on property: has characteristic
  some values from: PATO_0000018
editor preferred term: fluorescently labeled MHC multimer
has curation status: IAO_0000123
definition: 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

survival rate
type: Class
subclass of: measurement datum
editor preferred term: survival rate
has curation status: IAO_0000120
definition: 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.
term editor: Oliver He
definition source: adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate

recombinant BAC cloning
type: Class
subclass of: OBI_0600064
editor preferred term: recombinant BAC cloning
has curation status: IAO_0000123
definition: 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
definition source: http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome

multiple testing correction objective
type: Class
subclass of: OBI_0200186
editor preferred term: multiple testing correction objective
example of usage: Application of the Bonferroni correction
has curation status: IAO_0000120
definition: A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
alternative label: multiple comparison correction objective
definition source: http://en.wikipedia.org/wiki/Multiple_Testing_Correction

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200188
subclass of: OBI_0200171
editor preferred term: statistical model validation
example of usage: 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
has curation status: IAO_0000120
definition: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
term editor: Helen Parkinson
definition source: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29

double blind study execution
type: Class
equivalent class: Class
  intersection of: treatment portion of study execution
  intersection of: Restriction
    on property: has part
    all values from: Class
      complement of: Class
        union of: informing investigator of subject study arm
        union of: informing subject of study arm
subclass of: single blind study execution
editor preferred term: double blind study execution
has curation status: IAO_0000120
definition: 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
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#double
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

obsolete transcription factor binding site
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete transcription factor binding site
has curation status: IAO_0000002
definition source: SO:0000235
has obsolescence reason: IAO_0000228
curator note: PLace_holder for sequence ontology term
term tracker item: https://github.com/obi-ontology/obi/issues/1553
term replaced by: SO_0000235
deprecated: true

glucometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: glucometer
example of usage: Diabetic patients use glucometers to determine their glucose levels
has curation status: IAO_0000122
definition: A measurement device with the function to measure and record the level/amount of glucose in a blood sample
term editor: PERSON:Frank Gibson
term editor: PERSON:Helen Parkinson
alternative label: glucose meter
definition source: http://en.wikipedia.org/wiki/Glucose_meter

purification objective
type: Class
subclass of: separation into different composition objective
editor preferred term: purification objective
example of usage: the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
has curation status: IAO_0000120
definition: 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
term editor: PERSON:Bjoern Peters
alternative label: isolation objective
definition source: BP
curator note: 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality

obsolete_primary structure of protein
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_primary structure of protein
example of usage: SIINFEKL' is the primary structure of a peptide
has curation status: IAO_0000123
definition: The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together
term editor: Person:Bjoern Peters
has obsolescence reason: IAO_0000228
deprecated: true

capsule shell
type: Class
subclass of: material entity
editor preferred term: capsule shell
has curation status: IAO_0000120
definition: a small rounded gelatinous container
term editor: Person:Alan Ruttenberg
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

recombinant phage cloning
type: Class
subclass of: OBI_0600064
editor preferred term: recombinant phage cloning
example of usage: Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
has curation status: IAO_0000120
definition: 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.
term editor: Helen Parkinson
definition source: http://www.ncbi.nlm.nih.gov/books/bv.fcgi

cross linking
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified output
  some values from: molecular entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: cross linking
example of usage: cross linking can be used as a probe to link proteins together, to check protein protein interactions
has curation status: IAO_0000120
definition: A process in which bonds are created that link one polymer to another
term editor: PERSON: Chris Stoeckert
definition source: http://en.wikipedia.org/wiki/Cross-link

spike train datum
type: Class
subclass of: measurement datum
editor preferred term: spike train datum
example of usage: Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
has curation status: IAO_0000120
definition: A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
editor note: needs more work to see exactly what the data set looks like - HP
term editor: Helen Parkinson, Alan Ruttenberg
alternative label: spike train measurement
definition source: Jessica Turner, NIF

prothrombin time assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: scalar measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: blood coagulation
editor preferred term: prothrombin time assay
example of usage: PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
has curation status: IAO_0000120
definition: An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample.
term editor: Alan Ruttenberg
definition source: url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06

denaturing
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: nucleic acid
    union of: PR_000000001
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: denaturing
example of usage: Denaturing DNA in alcohol
has curation status: IAO_0000123
definition: Is a process in which the tertiary or secondary structure of a polymer is disrupted
definition source: http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29

informing investigator of subject study arm
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Restriction
      on property: denotes
      some values from: Restriction
        on property: has characteristic
        some values from: participant under investigation role
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property: has role
      some values from: investigation agent role
editor preferred term: informing investigator of subject study arm
example of usage: Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound.
has curation status: IAO_0000120
definition: A planned process with the objective to make the investigator aware of which study arm a patient is participating in.
editor note: 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
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

antithrombin-III berichrome assay
type: Class
subclass of: human antithrombin-III in blood assay
subclass of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: scalar measurement datum
  intersection of: Restriction
    on property: has participant
    some values from: Berichrom(r) Antithrombin III (A) Kit
  intersection of: Restriction
    on property: has specified output
    cardinality: 1
editor preferred term: antithrombin-III berichrome assay
has curation status: IAO_0000120
definition: An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard
alternative label: AT-III assay
definition source: url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06

material maintenance objective
type: Class
subclass of: objective specification
editor preferred term: material maintenance objective
has curation status: IAO_0000122
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters

presentation of stimulus
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: OBI_0100026
    intersection of: Restriction
      on property: has role
      some values from: participant under investigation role
editor preferred term: presentation of stimulus
example of usage: The presentation of a flashing light to a monkey during reward training
has curation status: IAO_0000120
definition: A planned process with the objective to expose an organism to a stimulus.
term editor: Helen Parkinson, Jessica Turner, Dirk Derom
alternative label: stimulation of organism
definition source: Helen Parkinson, Jessica Turner, Dirk Derom

spectrolyse heparin antifactor-Xa assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: scalar measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: blood coagulation
editor preferred term: spectrolyse heparin antifactor-Xa assay
example of usage: PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
has curation status: IAO_0000120
definition: An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration.
term editor: Alan Ruttenberg
definition source: url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06

amplified DNA
type: Class
equivalent class: Class
  intersection of: deoxyribonucleic acid
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600058
subclass of: deoxyribonucleic acid
subclass of: processed material
editor preferred term: amplified DNA
example of usage: Amplied DNA created by PCR
has curation status: IAO_0000122
definition: DNA that has been produced in an enzymatic amplification process
term editor: PERSON: Alan Ruttenberg
definition source: Alan Ruttenberg

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
editor preferred term: informed consent process
has curation status: IAO_0000122
definition: 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.
editor note: 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.
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: characteristic of
    some values from: deoxyribonucleic acid
subclass of: SO_0000001
editor preferred term: primary structure of DNA macromolecule
has curation status: IAO_0000123
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
term editor: BP et al

measuring neural activity in the caudate nucleus assay
type: Class
subclass of: extracellular electrophysiology recording assay
editor preferred term: measuring neural activity in the caudate nucleus assay
example of usage: An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus
has curation status: IAO_0000120
definition: An assay that measures neural activity in the caudate nucleus
term editor: Helen Parkinson
definition source: Dirk Derom, OBI
definition source: Jessica Turner, NIF

to be treated with active ingredient role
type: Class
subclass of: participant under investigation role
editor preferred term: to be treated with active ingredient role
example of usage: Role of a patient in a group treated with an active substance in a clinical trial
has curation status: IAO_0000122
definition: 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
term editor: Person:Alan Ruttenberg
definition source: PERSON: Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

guar gum
type: Class
subclass of: material entity
editor preferred term: guar gum
has curation status: IAO_0000120
definition: 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.
term editor: Helen Parkinson
definition source: http://en.wikipedia.org/wiki/Guar_gum

Berichrom(r) Antithrombin III (A) Kit
type: Class
subclass of: processed material
editor preferred term: Berichrom(r) Antithrombin III (A) Kit
has curation status: IAO_0000120
definition: 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
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

micro electrode
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: micro electrode
example of usage: A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
has curation status: IAO_0000120
definition: An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
term editor: Helen Parkinson, Jessica Turner, Dirk Derom
alternative label: micro electrode measuring device
definition source: Jessica Turner, Dirk Derom

fucoidan
type: Class
subclass of: molecular entity
editor preferred term: fucoidan
has curation status: IAO_0000120
definition: 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).
term editor: Helen Parkinson
definition source: http://en.wikipedia.org/wiki/Fucoidan

calibration
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: assay
subclass of: Restriction
  on property: has specified output
  some values from: measurement device
editor preferred term: calibration
example of usage: the process of using pH buffer adjust a pH meter
has curation status: IAO_0000122
definition: 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.
term editor: GROUP: OBI Philly workshop
definition source: WEB:http://en.wikipedia.org/wiki/calibration

anticoagulant tube storage of blood specimen
type: Class
subclass of: OBI_0302893
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      intersection of: anticoagulant-containing test tube
      intersection of: Restriction
        on property: surrounded by
        some values from: OBI_0100017
editor preferred term: anticoagulant tube storage of blood specimen
has curation status: IAO_0000120
definition: Storage of a blood specimen in a tube with anticoagulant
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

activated partial thromboplastin time assay
type: Class
subclass of: OBI_0003040
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Class
        union of: blood specimen
        union of: OBI_0100016
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: time measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: blood coagulation
editor preferred term: activated partial thromboplastin time assay
example of usage: The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660)
has curation status: IAO_0000120
definition: An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy.
editor note: There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant).
term editor: Alan Ruttenberg
term editor: OBI call
alternative label: aPTT assay
definition source: url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310

filled capsule
type: Class
subclass of: pill
subclass of: Restriction
  on property: has part
  some values from: capsule shell
editor preferred term: filled capsule
has curation status: IAO_0000120
definition: A pill in the form of a small rounded gelatinous container with medicine inside.
term editor: Person:Alan Ruttenberg
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

single blind study execution
type: Class
equivalent class: Class
  intersection of: treatment portion of study execution
  intersection of: Restriction
    on property: has part
    all values from: Class
      complement of: informing subject of study arm
subclass of: treatment portion of study execution
editor preferred term: single blind study execution
has curation status: IAO_0000120
definition: 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
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#single
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

thrombin time assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: scalar measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: blood coagulation
editor preferred term: thrombin time assay
example of usage: PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
has curation status: IAO_0000120
definition: An assay that measures the time between the addition of the thrombin and the clot formation in plasma.
term editor: Alan Ruttenberg
definition source: url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06

recombinant YAC cloning
type: Class
subclass of: OBI_0600064
editor preferred term: recombinant YAC cloning
example of usage: Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
has curation status: IAO_0000123
definition: 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
term editor: Helen Parkinson
definition source: http://www.ncbi.nlm.nih.gov/books/bv.fcgi

to be treated with placebo role
type: Class
subclass of: participant under investigation role
editor preferred term: to be treated with placebo role
has curation status: IAO_0000120
definition: 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
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

treatment portion of study execution
type: Class
subclass of: planned process
subclass of: Restriction
  on property: part of
  some values from: study design execution
editor preferred term: treatment portion of study execution
has curation status: IAO_0000120
definition: A planned process, part of a study design execution, during which the treatment of subjects is ongoing
editor note: 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

pill
type: Class
subclass of: processed material
editor preferred term: pill
has curation status: IAO_0000120
definition: A dose of medicine or placebo in the form of a small pellet.
term editor: Person:Alan Ruttenberg
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

research organization
type: Class
subclass of: organization
editor preferred term: research organization
example of usage: The SALK institute is a research organization.
has curation status: IAO_0000123
definition: An organization formed with a goal to have its members conduct investigations
term editor: Person:Bjoern Peters

obsolete_primary structure of sequence macromolecule
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_primary structure of sequence macromolecule
has curation status: IAO_0000123
definition: A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
term editor: Person:Bjoern Peters
has obsolescence reason: IAO_0000228
deprecated: true

DNA residue methylation
type: Class
subclass of: PATO_0001241
editor preferred term: DNA residue methylation
has curation status: IAO_0000123
definition: a quality of a DNA residue that has a methyl group attached to it

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
editor preferred term: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: IAO_0000122
definition: A device in which a measure function inheres.
term editor: GROUP:OBI Philly workshop
definition source: OBI

high molecular weight DNA extract
type: Class
subclass of: DNA extract
editor preferred term: high molecular weight DNA extract
example of usage: Extraction of chromosomal DNA from mammalian cells by first isolating nucei
has curation status: IAO_0000120
definition: The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
term editor: PERSON:Chris Stoeckert
definition source: OBI

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
editor preferred term: manufacturer
has curation status: IAO_0000123
definition: A person or organization that has a manufacturer role.

test tube
type: Class
subclass of: vial
subclass of: Restriction
  on property: has function
  some values from: contain function
editor preferred term: test tube
has curation status: IAO_0000120
definition: A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
term editor: Bjoern Peters
alternative label: collection tube
alternative label: sample tube
definition source: http://en.wikipedia.org/wiki/Test_tube

oral ingestion of pill
type: Class
equivalent class: Class
  intersection of: oral administration
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: role of
        some values from: pill
  intersection of: Restriction
    on property: has specified input
    some values from: pill
subclass of: oral administration
editor preferred term: oral ingestion of pill
has curation status: IAO_0000123
definition: An adding a material entity to target with the entity is a pill and the target is the mouth
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred term: material maintenance
has curation status: IAO_0000123
definition: A planned process with the objective to maintain some or all of the characteristics of an input material over time.

labeled oligonucleotide
type: Class
subclass of: OBI_0001936
subclass of: Restriction
  on property: has part
  some values from: OBI_0002744
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0600038
editor preferred term: labeled oligonucleotide
has curation status: IAO_0000123
definition: 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
editor note: 2010-01-31: Philippe Rocca-Serra placeholder
term editor: Person: Philippe Rocca-Serra

unblinding process
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: study design execution
  intersection of: Restriction
    on property: part of
    some values from: informing subject of study arm
editor preferred term: unblinding process
has curation status: IAO_0000120
definition: 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.
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

subject agrees they understand informed consent document
type: Class
subclass of: planned process
subclass of: Restriction
  on property: part of
  some values from: informed consent process
editor preferred term: subject agrees they understand informed consent document
has curation status: IAO_0000120
definition: A planned process in which a subject receives an informed consent document and agrees that they have understood it.
editor note: 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
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

informing subject of study arm
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: informed consent process
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property: has role
      some values from: participant under investigation role
editor preferred term: informing subject of study arm
example of usage: Informing participants whether they are receiving a placebo or a treatment with an investigational compound.
has curation status: IAO_0000120
definition: A planned process with the objective to make the subject aware of which study arm they are participating in.
editor note: 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
term editor: Person:Alan Ruttenberg
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

Sysmex CA-6000 Coagulation Analyzer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000829
editor preferred term: Sysmex CA-6000 Coagulation Analyzer
has curation status: IAO_0000120
definition: The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
term editor: Person:Alan Ruttenberg
definition source: web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

obsolete hospital
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete hospital
example of usage: human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
has curation status: IAO_0000120
definition: A medical organization at which sick or injured people are given clinical care
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
definition source: modified from the wording of the wordnet definition; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
has obsolescence reason: IAO_0000228
term tracker item: https://github.com/obi-ontology/obi/issues/1295
term replaced by: OMRSE_00000056
deprecated: true

primary structure of RNA molecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: characteristic of
    some values from: ribonucleic acid
subclass of: SO_0000001
editor preferred term: primary structure of RNA molecule
has curation status: IAO_0000123
definition: 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
term editor: Person:Bjoern Peters

test substance role
type: Class
subclass of: role
editor preferred term: test substance role
example of usage: fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
has curation status: IAO_0000120
definition: 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
term editor: Person:Alan Ruttenberg
definition source: Group:OBI

polyA RNA extraction
type: Class
subclass of: OBI_0666666
editor preferred term: polyA RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group

organellar RNA extraction
type: Class
subclass of: OBI_0666666
editor preferred term: organellar RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which the desired output material is RNA in the organelle(s).
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group

obsolete_diethyl pyrocarbonate
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_diethyl pyrocarbonate
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228
deprecated: true

record of missing knowledge
type: Class
subclass of: information content entity
editor preferred term: record of missing knowledge
example of usage: 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.
has curation status: IAO_0000120
definition: An information content entity created to indicate that information about something is not available to the person recording it.
editor note: 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.
term editor: Bjoern Peters

western blot assay
type: Class
subclass of: OBI_0001978
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: peptide
  intersection of: Restriction
    on property: has specified input
    some values from: peptide
editor preferred term: western blot assay
example of usage: Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest.
has curation status: IAO_0000120
definition: An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules.
term editor: IEDB
term editor: Philippe Rocca-Serra
definition source: IEDB
definition source: Philippe Rocca-Serra

total RNA extraction
type: Class
subclass of: OBI_0666666
editor preferred term: total RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which total cellular and organelle RNA are extracted.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group

obsolete intracellular material detection by flow cytometry assay
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete intracellular material detection by flow cytometry assay
has curation status: IAO_0000123
definition: An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
has obsolescence reason: IAO_0000227
term replaced by: flow cytometry assay
IEDB alternative term: intracellular staining
deprecated: true

complementary nucleotide probe role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: nucleic acid
editor preferred term: complementary nucleotide probe role
example of usage: A primer in a PCR reaction. A probe on an Affymetrix chip.
has curation status: IAO_0000120
definition: 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
term editor: PERSON:Bjoern Peters

record of unknown sex
type: Class
subclass of: record of missing knowledge
subclass of: Restriction
  on property: is about
  some values from: PATO_0000047
editor preferred term: record of unknown sex
example of usage: 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.
has curation status: IAO_0000120
definition: a record indicating that the biological sex of an organism is not known.
editor note: 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.
term editor: Bjoern Peters

cytoplasmic RNA extraction
type: Class
subclass of: OBI_0666666
editor preferred term: cytoplasmic RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which the desired output material is RNA in the cytoplasm.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group

northern blot assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: ribonucleic acid
  intersection of: Restriction
    on property: has specified input
    some values from: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
editor preferred term: northern blot assay
example of usage: The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay.
has curation status: IAO_0000123
definition: An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
alternative label: northern blot

Likelihood-ratio test
type: Class
subclass of: OBI_0200000
editor preferred term: Likelihood-ratio test
has curation status: IAO_0000123
definition: 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.
term editor: Tina Boussard

nuclear RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is specified output of
  some values from: nuclear RNA extraction
editor preferred term: nuclear RNA extract
example of usage: 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)
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group

96-well neutralization assay
type: Class
subclass of: serum neutralization of viral infectivity assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400076
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400076
editor preferred term: 96-well neutralization assay
has curation status: IAO_0000120
definition: A serum neutralization of viral infectivity assay which is performed in a 96-well plate.
term editor: Bjoern Peters
term editor: Melanie Courtot
alternative label: microneutralization assay

establishing cancer cell line
type: Class
subclass of: OBI_0001867
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0001906
editor preferred term: establishing cancer cell line
example of usage: Establishment of HeLa immortal cell line
has curation status: IAO_0000123
definition: 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
comment: Helen Parkinson

pattern matching objective
type: Class
subclass of: OBI_0200166
editor preferred term: pattern matching objective
has curation status: IAO_0000123
definition: 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.
term editor: Tina Boussard
definition source: http://en.wikipedia.org/wiki/Pattern_matching

polyA RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is specified output of
  some values from: polyA RNA extraction
editor preferred term: polyA RNA extract
example of usage: 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.)
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group

single-nucleotide-resolution nucleic acid structure mapping assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: assay
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay
has curation status: IAO_0000120
definition: An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
term editor: Philippe Rocca-Serra
definition source: RNAO

viral hemagglutination assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: has part
  some values from: induced hemagglutination
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
editor preferred term: viral hemagglutination assay
example of usage: Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells.
has curation status: IAO_0000120
definition: An assay that quantifies viruses by their hemagglutination activity.
term editor: Bjoern Peters
term editor: Melanie Courtot
term editor: Randi Vita
alternative label: HA
alternative label: HI
alternative label: viral haemagglutinin assay
definition source: url:http://en.wikipedia.org/wiki/Hemagglutination_assay

serum neutralization of viral infectivity assay
type: Class
subclass of: analyte assay
subclass of: OBI_0003040
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: OBI_0100017
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100017
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: Viruses
  intersection of: Restriction
    on property: has specified input
    some values from: Viruses
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: immunoglobulin-mediated neutralization
editor preferred term: serum neutralization of viral infectivity assay
has curation status: IAO_0000120
definition: An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
term editor: Bjoern Peters
term editor: Melanie Courtot
alternative label: influenza neutralization assay
definition source: url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/

pre-mortem specimen
type: Class
equivalent class: Class
  intersection of: specimen with pre- or post-mortem status
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen with pre- or post-mortem status
editor preferred term: pre-mortem specimen
example of usage: material obtained through a liver biopsy from a human patient
has curation status: IAO_0000120
definition: a specimen that was taken from a live organism
term editor: Bjoern Peters
definition source: MO_705 premortem

detection of specific nucleic acid polymers with complementary probes
type: Class
equivalent class: Class
  intersection of: analyte assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: nucleic acid
        intersection of: Restriction
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: analyte role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: nucleic acid
subclass of: analyte assay
editor preferred term: detection of specific nucleic acid polymers with complementary probes
example of usage: Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays.
has curation status: IAO_0000120
definition: An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
term editor: IEDB
definition source: IEDB

viral hemagglutination inhibition assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: Viruses
  intersection of: Restriction
    on property: has specified input
    some values from: Viruses
subclass of: Restriction
  on property: has part
  some values from: induced hemagglutination
editor preferred term: viral hemagglutination inhibition assay
example of usage: Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody.
has curation status: IAO_0000120
definition: An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors.
term editor: Bjoern Peters
term editor: Melanie Courtot
term editor: Randi Vita
alternative label: HAI
alternative label: HIA
alternative label: biological activity
alternative label: hemagglutination inhibition
alternative label: viral haemagglutinin inhibition assay
definition source: OBI branch derived

cytoplasmic RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: cytoplasmic RNA extraction
subclass of: RNA extract
editor preferred term: cytoplasmic RNA extract
example of usage: 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.)
has curation status: IAO_0000120
definition: A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
term editor: PERSON:Chris Stoeckert
definition source: UPenn Group

cell line immortalization
type: Class
subclass of: OBI_0001867
subclass of: Restriction
  on property: has part
  some values from: OBI_0001907
subclass of: Restriction
  on property: has specified output
  some values from: immortal cell line
editor preferred term: cell line immortalization
example of usage: Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
has curation status: IAO_0000123
definition: 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
editor note: 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.
term editor: Bjoern Peters
alternative label: 'establishing immortal cell line through directed genetic modification'
definition source: OBI
comment: A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line.

random primed DNA labeling
type: Class
subclass of: OBI_0600038
editor preferred term: random primed DNA labeling
example of usage: PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
has curation status: IAO_0000120
definition: a labeling in which random primers are used to uniformly label input DNA
editor note: need to add Klenow subunit of DNA polymerase I under material entity
term editor: Person: Bjoern Peters Person: Chris Stoeckert
term editor: Person: Philippe Rocca-Serra
definition source: PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13.

RNA extract
type: Class
equivalent class: Class
  intersection of: nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0666666
  intersection of: Restriction
    on property: has grain
    some values from: ribonucleic acid
subclass of: nucleic acid extract
editor preferred term: RNA extract
has curation status: IAO_0000120
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: Group: UPenn Group

cell-cell killing assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Restriction
    on property: has specified input
    some values from: cell
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: cell killing
subclass of: OBI_0001977
editor preferred term: cell-cell killing assay
example of usage: Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
has curation status: IAO_0000120
definition: A cytometry assay that monitors a cell population to track how many are killed by other cells.
term editor: IEDB
definition source: IEDB

in vivo cell killing assay
type: Class
equivalent class: Class
  intersection of: cell-cell killing assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: cell-cell killing assay
editor preferred term: in vivo cell killing assay
example of usage: Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells.
has curation status: IAO_0000120
definition: A cell killing assay that measures if and how many target cells are killed within an organism.
term editor: IEDB
definition source: IEDB

secondary structure of sequence macromolecule
type: Class
subclass of: PATO_0001241
editor preferred term: secondary structure of sequence macromolecule
has curation status: IAO_0000002
definition: 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.
editor note: 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
term editor: Person: Philippe Rocca-Serra
definition source: Wikipedia

nuclear RNA extraction
type: Class
subclass of: OBI_0666666
editor preferred term: nuclear RNA extraction
has curation status: IAO_0000120
definition: A RNA extraction process in which the desired output material is RNA in the nucleus.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group

survival curve
type: Class
subclass of: line graph
subclass of: Restriction
  on property: is about
  some values from: survival rate
editor preferred term: survival curve
has curation status: IAO_0000122
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm

cell proliferation assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: cell population proliferation
subclass of: OBI_0001977
editor preferred term: cell proliferation assay
example of usage: Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
has curation status: IAO_0000120
definition: A cytometry assay which measures the degreee to which input cells are replicating.
term editor: IEDB
definition source: IEDB

Southern blot assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: deoxyribonucleic acid
  intersection of: Restriction
    on property: has specified input
    some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has part
  some values from: OBI_0302903
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: detection of specific nucleic acid polymers with complementary probes
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: site
editor preferred term: Southern blot assay
example of usage: PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing.
has curation status: IAO_0000120
definition: An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity.
term editor: Marcus Chibucos
term editor: Philippe Rocca-Serra
alternative label: Southern blot
definition source: OBI

real time polymerase chain reaction assay
type: Class
subclass of: OBI_0002692
subclass of: Restriction
  on property: has part
  some values from: polymerase chain reaction
editor preferred term: real time polymerase chain reaction assay
has curation status: IAO_0000120
definition: An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
term editor: Bjoern Peters
term editor: Melanie Courtot
alternative label: Q-PCR
alternative label: kinetic polymerase chain reaction
alternative label: qPCR
alternative label: quantitative real time polymerase chain reaction
definition source: url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

protein extract
type: Class
subclass of: extract
subclass of: Restriction
  on property: has part
  some values from: PR_000000001
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0302884
editor preferred term: protein extract
example of usage: 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.
has curation status: IAO_0000120
definition: 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,
term editor: Person: Philippe Rocca-Serra
definition source: OBI & wikipedia

total RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: total RNA extraction
subclass of: RNA extract
editor preferred term: total RNA extract
example of usage: Extraction of total RNA from cells with Qiagen mini RNeasy kit
has curation status: IAO_0000120
definition: A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group

secondary structure of RNA molecule
type: Class
subclass of: secondary structure of sequence macromolecule
editor preferred term: secondary structure of RNA molecule
example of usage: PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
has curation status: IAO_0000123
editor note: 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
term editor: Person: Philippe Rocca-Serra

DEPC structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: DEPC structure mapping assay
example of usage: PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe
term editor: Philippe Rocca-Serra
definition source: RNA ontology

organellar RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: organellar RNA extraction
subclass of: RNA extract
editor preferred term: organellar RNA extract
example of usage: Extraction of organellar RNA from plant cells using organellar RNA binding protein.
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group

post mortem specimen
type: Class
equivalent class: Class
  intersection of: specimen with pre- or post-mortem status
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen with pre- or post-mortem status
editor preferred term: post mortem specimen
example of usage: the spleen taken from a dead mouse
has curation status: IAO_0000120
definition: a specimen that was taken from a dead organism
term editor: Bjoern Peters
definition source: MO_416 postmortem

in vitro cell killing assay
type: Class
equivalent class: Class
  intersection of: cell-cell killing assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: OBI_0100060
        intersection of: Restriction
subclass of: cell-cell killing assay
subclass of: OBI_0003587
editor preferred term: in vitro cell killing assay
example of usage: Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
has curation status: IAO_0000120
definition: A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
term editor: IEDB
definition source: IEDB

reporter cell line analyte detection bioassay
type: Class
subclass of: analyte assay
subclass of: OBI_0003587
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: cell line
  intersection of: Restriction
    on property: has specified input
    some values from: cell line
subclass of: Restriction
  on property: has part
  some values from: OBI_0600024
editor preferred term: reporter cell line analyte detection bioassay
example of usage: CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant.
has curation status: IAO_0000120
definition: An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant.
term editor: IEDB
definition source: IEDB

sequence feature annotation
type: Class
subclass of: information content entity
editor preferred term: sequence feature annotation
has curation status: IAO_0000120
definition: Information about a sequence region
term editor: Bjoern Peters
definition source: Bjoern Peters
comment: place holder for sequence ontology term

induced hemagglutination
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: erythrocyte
editor preferred term: induced hemagglutination
has curation status: IAO_0000120
definition: The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
editor note: 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'.
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
alternative label: hemeagglutination
definition source: WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination

supplying
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: material entity
editor preferred term: supplying
example of usage: Jackson Labs supplies mouse strains.
has curation status: IAO_0000120
definition: A planned process with the objective to provide material entities to be used in an investigation.
term editor: Jennifer Fostel
definition source: Jennifer Fostel
curator note: 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.

labeled DNA extract
type: Class
equivalent class: Class
  intersection of: labeled nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has specified input
        some values from: DNA extract
  intersection of: Restriction
    on property: has grain
    some values from: deoxyribonucleic acid
subclass of: labeled nucleic acid extract
editor preferred term: labeled DNA extract
has curation status: IAO_0000120
definition: 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.
editor note: 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
term editor: Group: OBI group
definition source: Group: OBI group

cloacal specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: UBERON_0000162
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600005
subclass of: specimen from organism
editor preferred term: cell specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf

radio immuno assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: OBI_0002743
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has characteristic
        some values from: PATO_0001741
editor preferred term: radio immuno assay
example of usage: To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
has curation status: IAO_0000120
definition: An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody.
term editor: IEDB
definition source: IEDB

real time reverse-transcription polymerase chain reaction assay
type: Class
subclass of: OBI_0002692
subclass of: Restriction
  on property: has part
  some values from: OBI_0600028
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: real time polymerase chain reaction assay
    intersection of: OBI_0003368
subclass of: Restriction
  on property: has specified output
  some values from: information content entity
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: gene expression
editor preferred term: real time reverse-transcription polymerase chain reaction assay
has curation status: IAO_0000120
definition: An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay.
term editor: Bjoern Peters
term editor: Melanie Courtot
alternative label: RRT-PCR
alternative label: RT-rt PCR
alternative label: qRT-PCR

X-ray crystallography 3D molecular structure determination assay
type: Class
subclass of: OBI_0003117
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: X-ray source
  intersection of: Restriction
    on property: has specified input
    some values from: X-ray source
editor preferred term: X-ray crystallography 3D molecular structure determination assay
example of usage: Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
has curation status: IAO_0000120
definition: A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
term editor: IEDB
definition source: IEDB

promoter activity detection by reporter gene assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified input
  some values from: cell
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: core promoter sequence-specific DNA binding
editor preferred term: promoter activity detection by reporter gene assay
example of usage: A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
has curation status: IAO_0000120
definition: An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene.
term editor: IEDB
definition source: IEDB

nasopharyngeal aspirate specimen
type: Class
subclass of: OBI_2000007
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: UBERON_0001728
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0002785
editor preferred term: nasopharyngeal aspirate specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120
definition: A specimen which derives from nasopharyngeal mucosa after aspiration.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf

freezing storage
type: Class
subclass of: OBI_0302893
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: PATO_0001985
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: PATO_0001985
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: freezing storage
example of usage: a fozen pellet used for later assay
has curation status: IAO_0000120
definition: A storage process in temperature that maintenance the frozen status of the stored entities.
editor note: 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.
term editor: Person: Alan Ruttenberg, Mathias Brochhausen
definition source: MO_481 frozen_storage
definition source: OBI

flow cytometry assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400044
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: fluorescence detection assay
      intersection of: OBI_0003368
subclass of: OBI_0001977
editor preferred term: flow cytometry assay
example of usage: Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
has curation status: IAO_0000120
definition: A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
term editor: IEDB
alternative label: FACS
definition source: IEDB

nasal swab specimen
type: Class
equivalent class: Class
  intersection of: OBI_2000006
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0002600
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: UBERON_0001826
subclass of: OBI_0002599
subclass of: OBI_2000006
editor preferred term: nasal swab specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf

Dulbecco's modified Eagle medium
type: Class
subclass of: culture medium
subclass of: Class
  intersection of: Restriction
    on property: has grain
    some values from: glucose
  intersection of: Restriction
    on property: has grain
    some values from: amino acid
editor preferred term: Dulbecco's modified Eagle medium
has curation status: IAO_0000123
definition: A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
editor note: Logical definition should contain all components listed in textual definition at some point.
term editor: PERSON:Bjoern Peters
alternative label: D-MEM
alternative label: DMEM

animal euthanization
type: Class
subclass of: OBI_0600006
subclass of: Restriction
  on property: has specified input
  some values from: Vertebrata <vertebrates>
editor preferred term: animal euthanization
example of usage: Rats were euthanized with CO2
has curation status: IAO_0000120
definition: 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
term editor: Helen Parkinson and Melissa Haendel
alternative label: animal sacrifice
definition source: Melissa Haendel
comment: may later be refined with more specific list of organisms

cytometric bead array assay
type: Class
equivalent class: Class
  intersection of: analyte assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_1000207
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: fluorescence detection assay
      intersection of: OBI_0003368
subclass of: analyte assay
editor preferred term: cytometric bead array assay
example of usage: Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
has curation status: IAO_0000120
definition: An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest.
term editor: IEDB
alternative label: Luminex assay
definition source: IEDB

labeled RNA extract
type: Class
equivalent class: Class
  intersection of: labeled nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has specified input
        some values from: RNA extract
  intersection of: Restriction
    on property: has grain
    some values from: ribonucleic acid
subclass of: labeled nucleic acid extract
editor preferred term: labeled RNA extract
has curation status: IAO_0000120
definition: 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.
editor note: 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
term editor: Group: OBI group
definition source: Group: OBI group

frozen specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: freezing storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred term: frozen specimen
example of usage: Frozen blood plasma
has curation status: IAO_0000123
definition: A specimen that has been frozen in order to store it.
term editor: Person:Alan Ruttenberg
definition source: MO_610 frozen_sample

surface plasmon resonance binding assay
type: Class
subclass of: binding assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: surface plasmon resonance instrument
  intersection of: Restriction
    on property: has specified input
    some values from: surface plasmon resonance instrument
editor preferred term: surface plasmon resonance binding assay
example of usage: Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow.
has curation status: IAO_0000120
definition: A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction.
term editor: IEDB
definition source: IEDB

labeled specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: has part
    some values from: OBI_0002744
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0600038
subclass of: processed specimen
subclass of: OBI_0001936
editor preferred term: labeled specimen
has curation status: IAO_0000123
definition: A specimen that has been modified in order to be able to detect it in future experiments
editor note: added during call 3/1/2010
term editor: OBI group

infectious agent
type: Class
equivalent class: Restriction
  on property: has characteristic
  some values from: OBI_1110093
subclass of: OBI_0100026
editor preferred term: infectious agent
has curation status: IAO_0000123
definition: is a material entity bearing the disposition to infect an organism
term editor: IEDB
definition source: IEDB

obsolete_ambidexterious handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_ambidexterious handedness
has curation status: IAO_0000123
has obsolescence reason: IAO_0000103
deprecated: true

lyophilization storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: lyophilization storage
has curation status: IAO_0000123
definition: a storage process with input material entity and output freeze dried material for long time storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed

material combination function
type: Class
subclass of: function
editor preferred term: material combination function
example of usage: A stirrer has a material combination function
has curation status: IAO_0000120
definition: A material separation function is a function that decreases the resolution between two or more material entities.
term editor: Helen Parkinson
definition source: OBI

obsolete_training service provider role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_training service provider role
example of usage: EBI provides training on databases and tools and has a training service provider role
has curation status: IAO_0000123
definition: a service provider role which is realized by a servicer provider organization performing some training
term editor: PERSON:Helen Parkinson
definition source: OBI
has obsolescence reason: IAO_0000103
deprecated: true

calorimeter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: calorimeter
has curation status: IAO_0000120
definition: A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
term editor: PERSON:Bjoern Peters
alternative label: calorimetry instrument?
definition source: http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm

study intervention
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0100051
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0100051
subclass of: Restriction
  on property: part of
  some values from: Class
    intersection of: study design execution
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: intervention design
editor preferred term: study intervention
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Bjoern Peters
definition source: GROUP: OBI

material separation device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: material separation function
subclass of: device
editor preferred term: material separation device
example of usage: flow cytometer
has curation status: IAO_0000123
definition: A device with a separation function realized in a planed process

positron emission tomography scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
editor preferred term: positron emission tomography scanner
has curation status: IAO_0000120
definition: A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule.
term editor: PERSON:Bjoern Peters
alternative label: PET scanner?
definition source: http://en.wikipedia.org/wiki/Positron_emission_tomography

intramuscular injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0001134
subclass of: injection
subclass of: OBI_0600007
editor preferred term: intramuscular injection
has curation status: IAO_0000123
definition: is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe

micromanipulator
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: micromanipulator
has curation status: IAO_0000120
definition: A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand.
term editor: PERSON:Bjoern Peters
definition source: http://en.wikipedia.org/wiki/Micromanipulator

obsolete_material access provider role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_material access provider role
example of usage: A person or organization who provides access to a DNA sequencer.
has curation status: IAO_0000123
definition: a service provider role which is realized by a servicer provider organization performing access to some material
term editor: PERSON:Helen Parkinson
definition source: OBI
has obsolescence reason: IAO_0000103
deprecated: true

obsolete_left handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_left handedness
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228
deprecated: true

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001930
editor preferred term: categorical measurement datum
has curation status: IAO_0000120
definition: A measurement datum that is reported on a categorical scale.
term editor: Bjoern Peters
alternative label: nominal mesurement datum
definition source: Bjoern Peters

training process
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: training objective
subclass of: planned process
editor preferred term: training process
example of usage: e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
has curation status: IAO_0000123
definition: a process that achieves a training objective

optical microscope
type: Class
subclass of: OBI_0400169
editor preferred term: optical microscope
has curation status: IAO_0000120
definition: A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
term editor: PERSON:Bjoern Peters

service consumer role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
editor preferred term: service consumer role
example of usage: A biologist who uses a sequencing services fulfills the role of a service consumer
has curation status: IAO_0000120
definition: a role which inheres in a person who uses a service
term editor: Person:Helen Parkinson
definition source: OBI

intradermal injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0002067
subclass of: injection
subclass of: OBI_0600007
editor preferred term: intradermal injection
has curation status: IAO_0000123
definition: is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe
term editor: PERSON: Melanie Courtot

chemical cleavage
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100051
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: molecular entity
    intersection of: Restriction
      on property: has role
      some values from: reagent role
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: chemical cleavage
example of usage: 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.
has curation status: IAO_0000120
definition: 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
term editor: PERSON:Philippe Rocca-Serra
definition source: RNA ontology group

handedness assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: PATO_0002201
editor preferred term: handedness assay
example of usage: The Edinburgh handedness assay is a specific method of determing handedness
has curation status: IAO_0000120
definition: An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
term editor: Helen Parkinson
alternative label: handedness test
definition source: url:http://en.wikipedia.org/wiki/Handedness

vibration isolation table
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: vibration isolation table
has curation status: IAO_0000120
definition: A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
term editor: PERSON:Bjoern Peters
definition source: United States Patent 6877711

sterilization function
type: Class
subclass of: function
editor preferred term: sterilization function
has curation status: IAO_0000123
definition: a function to remove viable organisms from an input material

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: planned process
editor preferred term: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has curation status: IAO_0000123
definition: 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
term editor: PERSON:Helen Parkinson

oscilloscope
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: oscilloscope
has curation status: IAO_0000120
definition: A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis).
term editor: PERSON:Bjoern Peters
definition source: http://en.wikipedia.org/wiki/Oscilloscope

accessed material role
type: Class
subclass of: role
editor preferred term: accessed material role
example of usage: the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
has curation status: IAO_0000123
definition: is realized in a planned process where the bearer participates
editor note: 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

paraffin specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: paraffin storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred term: paraffin specimen
example of usage: liver tissue embedded in paraffin
has curation status: IAO_0000123
definition: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_990 paraffin_sample

compound treatment design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study intervention
        intersection of: administration of material to specimen
editor preferred term: compound treatment design
has curation status: IAO_0000120
definition: an intervention design in which the treatment is the administration of a compound
editor note: This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
term editor: PERSON: Bjoern Peters
definition source: MO_555 compound_treatment_design

oral administration
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0000165
subclass of: OBI_0600007
editor preferred term: oral administration
has curation status: IAO_0000123
definition: An administering substance in vivo into the mouth of an organism
term editor: PERSON: Melanie Courtot

processed specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Class
    intersection of: processed material
    intersection of: OBI_0100051
subclass of: processed material
subclass of: OBI_0100051
editor preferred term: processed specimen
has curation status: IAO_0000122
definition: A specimen that has been intentionally physically modified.
editor note: A tissue sample that has been sliced and stained for a histology study.
term editor: Bjoern Peters
definition source: Bjoern Peters

subcutaneous injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0002072
subclass of: injection
subclass of: OBI_0600007
editor preferred term: subcutaneous injection
has curation status: IAO_0000123
definition: is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
term editor: PERSON: Melanie Courtot

electrode puller
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: electrode puller
has curation status: IAO_0000120
definition: A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube.
term editor: PERSON:Bjoern Peters
definition source: http://faculty.plattsburgh.edu/donald.slish/Puller1.html

obsolete_handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_handedness
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228
term replaced by: PATO_0002201
deprecated: true

self reported handedness assessment
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has specified output
  some values from: categorical measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: PATO_0002201
editor preferred term: self reported handedness assessment
has curation status: IAO_0000123
definition: An assay where a person makes a statement that indicates what handedness he has from a choice of different categories.

vibrotome
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: OBI_0600014
editor preferred term: vibrotome
has curation status: IAO_0000123
definition: A preparation device that uses a vibrating razor blade to cut through tissue.

reagent application function
type: Class
subclass of: function
editor preferred term: reagent application function
example of usage: An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
has curation status: IAO_0000120
definition: A function that is realized when a reagent is automatically added to some research material.
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
curator note: 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?

addition of molecular tracer function
type: Class
subclass of: reagent application function
editor preferred term: addition of molecular tracer function
example of usage: Immunohistochemical labeling of tissue sections by an autostainer staining system.
has curation status: IAO_0000120
definition: A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen.
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
definition source: PERSON: Nicole Vasilevsky, Matthew Brush

training objective
type: Class
subclass of: objective specification
editor preferred term: training objective
example of usage: A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package
has curation status: IAO_0000120
definition: An objective specification which is fulfilled by the provision of some training.
term editor: Helen Parkinson
definition source: OBI

categorical label
type: Class
subclass of: datum label
editor preferred term: categorical label
example of usage: 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.
has curation status: IAO_0000120
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
term editor: Bjoern Peters
definition source: Bjoern Peters

in live cell assay
type: Class
subclass of: assay
editor preferred term: in live cell assay
has curation status: IAO_0000123
definition: An assay in which a measurement is made by observing entities located in a live cell.

lyophilized specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: lyophilization storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred term: lyophilized specimen
example of usage: freezing dried DNA
has curation status: IAO_0000123
definition: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_589 freeze_dried_sample

in live organism assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
editor preferred term: in live organism assay
example of usage: Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
has curation status: IAO_0000120
definition: An assay in which a measurement is made by observing entities located in an organism.
term editor: Bjoern Peters
alternative label: in vivo assay

container
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: contain function
subclass of: device
editor preferred term: container
has curation status: IAO_0000123
definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
term editor: PERSON: Bjoern Peters

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
disjoint with: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: reagent role
editor preferred term: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: IAO_0000122
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 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: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI development call 2012-12-17.

dose specification
type: Class
subclass of: directive information entity
editor preferred term: dose specification
example of usage: a protocol specifying to administer 1 ml of vaccine to a mouse
has curation status: IAO_0000123
definition: a directive information entity that describes the dose that will be administered to a target

scalar score from composite inputs
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is specified output of
  some values from: OBI_0200000
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
editor preferred term: scalar score from composite inputs
has curation status: IAO_0000120
definition: A measurement datum which is the result of combining multiple datum. For example, a mean or summary score.
editor note: JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question.
term editor: Person: Jessica Turner
alternative label: questionaire score
definition source: Person: Jessica Turner
curator note: JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?

fresh specimen
type: Class
subclass of: specimen with known storage state
editor preferred term: fresh specimen
example of usage: a liver freshly removed from a rat
has curation status: IAO_0000123
definition: a specimen that is output of a specimen creation process used for an investigation without storage.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_730 fresh_sample

obsolete_electrically powered device
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_electrically powered device
has curation status: IAO_0000123
definition: a processed material created to have a function and which requires electrical power to execute
has obsolescence reason: IAO_0000103
deprecated: true

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: SO_0000001
editor preferred term: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: IAO_0000120
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
term editor: Person:Chris Stoeckert
definition source: GROUP: OBI

obsolete_right handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_right handedness
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228
deprecated: true

cell-cell binding detection by flow cytometry assay
type: Class
equivalent class: Class
  intersection of: OBI_0001977
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: flow cytometry assay
      intersection of: OBI_0003368
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: OBI_0001588
subclass of: OBI_0001977
editor preferred term: cell-cell binding detection by flow cytometry assay
example of usage: Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates.
has curation status: IAO_0000120
definition: A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels.
term editor: IEDB
definition source: IEDB

handedness categorical measurement datum
type: Class
subclass of: categorical measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0002201
subclass of: Restriction
  on property: has category label
  some values from: Class
    one of: OBI_0000958
    one of: OBI_0000979
    one of: OBI_0000998
editor preferred term: handedness categorical measurement datum
has curation status: IAO_0000123
definition: 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
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Jessica Turner

paraffin storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: OBI_0100026
    union of: UBERON_0000465
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: paraffin storage
has curation status: IAO_0000120
definition: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
comment: need to specify paraffin or wax is one of specified input of the process

in container assay
type: Class
subclass of: assay
editor preferred term: in container assay
has curation status: IAO_0000123
definition: An assay in which a measurement is made by observing entities located in a container.

obsolete_protocol service provider role
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_protocol service provider role
example of usage: DNA sequencing of a sample by a core lab which returns data to the consumer
has curation status: IAO_0000120
definition: a service provider role which is realized by a servicer provider organization performing a protocol execution
term editor: PERSON:Helen Parkinson
has obsolescence reason: IAO_0000103
deprecated: true

agar stab specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: agar stab storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred term: agar stab specimen
has curation status: IAO_0000123
definition: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: MO_971 agar_stab

computed tomography scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
editor preferred term: computed tomography scanner
has curation status: IAO_0000120
definition: An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation.
term editor: PERSON:Bjoern Peters
alternative label: CT scanner
alternative label: X-ray computed tomography scanner
definition source: http://en.wikipedia.org/wiki/X-ray_computed_tomography

intranasal mucosal administration
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0005022
subclass of: OBI_0600007
editor preferred term: intranasal mucosal administration
has curation status: IAO_0000123
definition: The administration of a substance into the intranasal mucosis of an organism
term editor: PERSON: Melanie Courtot

dose
type: Class
subclass of: measurement datum
editor preferred term: dose
example of usage: An organism has been injected 1ml of vaccine
has curation status: IAO_0000123
definition: 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.

growth condition intervention design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: study intervention
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: growth environment
editor preferred term: growth condition intervention design
has curation status: IAO_0000120
definition: A study design in which the independent variable is the environmental condition in which the specimen is growing
term editor: PERSON: Bjoern Peters
definition source: MO_588 growth_condition_design

obsolete_DNA sequencing training service
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_DNA sequencing training service
has curation status: IAO_0000123
definition: A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
has obsolescence reason: IAO_0000103
deprecated: true

obsolete_general scalar measurement datum
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_general scalar measurement datum
has curation status: IAO_0000124
has obsolescence reason: IAO_0000103
deprecated: true

obsolete performing a diagnosis
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete performing a diagnosis
example of usage: Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.
has curation status: IAO_0000123
definition: The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
has obsolescence reason: IAO_0000103
term tracker item: https://github.com/obi-ontology/obi/issues/623
deprecated: true

PCR instrument
type: Class
subclass of: OBI_0400116
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: polymerase chain reaction
editor preferred term: PCR instrument
has curation status: IAO_0000123
definition: A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
editor note: 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.

electron microscope
type: Class
subclass of: OBI_0400169
editor preferred term: electron microscope
has curation status: IAO_0000123
definition: A microscope that produces an image of an object by targeting it with an electron beam

Edinburgh score
type: Class
subclass of: scalar score from composite inputs
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0002201
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
editor preferred term: Edinburgh score
has curation status: IAO_0000123
definition: A score that measures the dominance of a person's right or left hand in everyday activities.
term editor: Person: Alan Ruttenberg
term editor: Person:Jessica Turner
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html

DNA sequencing service
type: Class
equivalent class: Class
  intersection of: OBI_0001904
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: DNA sequencing assay
subclass of: OBI_0001904
subclass of: Restriction
  on property: realizes
  some values from: service consumer role
subclass of: Restriction
  on property: realizes
  some values from: service provider role
editor preferred term: DNA sequencing service
has curation status: IAO_0000123
definition: A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
editor note: Eagle-i will supply better English definition

service provision objective
type: Class
subclass of: objective specification
editor preferred term: service provision objective
example of usage: A sequencing centre has a service provision objective
has curation status: IAO_0000120
definition: An objective which is fulfilled by the provision of some service e.g. a training service
term editor: Helen Parkinson
definition source: OBI

intravenous injection
type: Class
equivalent class: Class
  intersection of: OBI_0600007
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0001638
subclass of: injection
subclass of: OBI_0600007
editor preferred term: intravenous injection
has curation status: IAO_0000123
definition: is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
term editor: PERSON: Melanie Courtot

administration of material to specimen
type: Class
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: target of material addition role
    intersection of: Restriction
      on property: role of
      some values from: OBI_0100051
editor preferred term: administration of material to specimen
example of usage: Staining cells in a tissue slice with a dye.
has curation status: IAO_0000120
definition: The directed combination of a material entity with a specimen.
term editor: Bjoern Peters
definition source: Bjoern Peters

device creation objective
type: Class
subclass of: material transformation objective
editor preferred term: device creation objective
has curation status: IAO_0000120
definition: an objective which aims to create a device with a specified function
term editor: PERSON: Helen Parkinson
definition source: OBI

growth environment
type: Class
subclass of: material entity
editor preferred term: growth environment
has curation status: IAO_0000120
definition: The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
editor note: Right now this may be incomplete. Should also cover e.g. sound, light as well.
term editor: PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
definition source: OBI group

questionnaire
type: Class
subclass of: document
editor preferred term: questionnaire
has curation status: IAO_0000120
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
term editor: PERSON: Jessica Turner
definition source: Merriam-Webster

Edinburgh handedness assay
type: Class
subclass of: handedness assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: Homo sapiens
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: Edinburgh score
subclass of: Restriction
  on property: has specified input
  has value: OBI_0001004
editor preferred term: Edinburgh handedness assay
example of usage: Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"
has curation status: IAO_0000120
definition: An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
term editor: Alan Ruttenberg
term editor: Gully Burns (orcid:0000-0003-1493-865X)
term editor: Jessica Turner
definition source: PMID:5146491
definition source: url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory

Faraday cage
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: Faraday cage
has curation status: IAO_0000120
definition: A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
term editor: PERSON:Bjoern Peters
alternative label: Faraday shield
definition source: Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
curator note: isolation function? HP

agar stab storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred term: agar stab storage
has curation status: IAO_0000120
definition: a storage process with input cell culture and agar and output agar stab for long time storage
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
comment: need to specify that agar is one of input for this process

RNASE CL3 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000025478
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025478
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: RNASE CL3 structure mapping assay
example of usage: PMID:16453415
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using RNAse CL3
definition source: RNA ontology

CMCT structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: CMCT structure mapping assay
example of usage: PMID:2422386 and PMID:2446263
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using CMCT probe
definition source: RNA ontology

image creation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: image
editor preferred term: image acquisition
example of usage: Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
has curation status: IAO_0000123
definition: A planned process that captures an image of an object.
term editor: PERSON: Jie Zheng
alternative label: image acquisition

MPE-Fe(II) structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: MPE-Fe(II) structure mapping assay
example of usage: PMID:6209709
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using Fe-MP probe
definition source: RNA ontology

obsolete_qualitative binding detection assay
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_qualitative binding detection assay
has curation status: IAO_0000123
definition: A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context.
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
has obsolescence reason: IAO_0000103
deprecated: true

nucleic acid extract
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: OBI_0666667
subclass of: processed specimen
editor preferred term: nucleic acid extract
has curation status: IAO_0000120
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
term editor: Person: Jie Zheng
definition source: UPenn Group

ENU structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: ENU structure mapping assay
example of usage: PMID:7002606 and PMID:2446263
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using ENU probe
definition source: RNA ontology

RNASE V1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000025477
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025477
subclass of: Restriction
  on property: has specified output
  some values from: secondary structure of RNA molecule
editor preferred term: RNASE V1 structure mapping assay
example of usage: PMID:7031604
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using RNAse V1
definition source: RNA ontology

kethoxal structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: kethoxal structure mapping assay
example of usage: single nucleotide resolution mapping assay using Kethoxal probe
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe
term editor: Philippe Rocca-Serra
definition source: RNA ontology

single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
type: Class
equivalent class: Class
  intersection of: single-nucleotide-resolution nucleic acid structure mapping assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: enzyme
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes.
term editor: Philippe Rocca-Serra
definition source: RNAO and OBI
term tracker item: https://github.com/obi-ontology/obi/issues/808

DMS structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: DMS structure mapping assay
example of usage: PMID:6159633 and PMID:2446263
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using DMS probe
definition source: RNA Ontology

DNASE 1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000006592
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000006592
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: DNASE 1 structure mapping assay
example of usage: PMID:3773731
has curation status: IAO_0000122
definition: A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
term editor: Philippe Rocca-Serra
alternative label: DNAse footprinting assay
alternative label: single nucleotide resolution mapping assay using DNAse I
definition source: RNA ontology

single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
type: Class
equivalent class: Class
  intersection of: single-nucleotide-resolution nucleic acid structure mapping assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: reagent role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: molecular entity
        intersection of: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes.
term editor: Philippe Rocca-Serra
definition source: RNAO and OBI

Rhodium DNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: Rhodium DNA structure mapping assay
example of usage: PMID:2843807
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using Rhodium probe
definition source: RNA ontology

RNA ADA I RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000003745
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000003745
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: RNA ADA I RNA structure mapping assay
example of usage: PMID:7527340
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using RNA adenosine deaminase I
definition source: RNA ontology

Lead structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: Lead structure mapping assay
example of usage: PMID:2686708
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using Lead probe
definition source: RNA ontology

RNASE T2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000014060
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000014060
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: RNASE T2 structure mapping assay
example of usage: PMID:6207483
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using RNAse T2
definition source: RNA ontology

gene dosage assay
type: Class
subclass of: assay
editor preferred term: gene dosage assay
has curation status: IAO_0000120
definition: An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene.
term editor: Bjoern Peters
definition source: David Osumi Sutherland

Fe-BABE RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: Fe-BABE RNA structure mapping assay
example of usage: PMID: 7862644
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using Fe-BABE probe
definition source: RNA ontology

RNASE U2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000025475
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025475
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: RNASE U2 structure mapping assay
example of usage: PMID:409999
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using RNAse U2
definition source: RNA ontology

binding constant determination assay
type: Class
subclass of: binding assay
subclass of: Restriction
  on property: has specified output
  some values from: binding constant
editor preferred term: binding constant determination assay
example of usage: Determination of KD value for an antibody binding a protein using a BIACORE assay.
has curation status: IAO_0000123
definition: A binding assay where the specified output is a binding constant
term editor: Bjoern Peters
term editor: Jason Greenbaum
term editor: Randi Vita
definition source: IEDB

NMIA RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: NMIA RNA structure mapping assay
example of usage: PMID: 15796531
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe
term editor: Philippe Rocca-Serra
alternative label: SHAPE mapping assay
alternative label: single nucleotide resolution mapping assay using NMIA probe
definition source: RNA ontology

Terbium RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: Terbium RNA structure mapping assay
example of usage: PMID:10772868
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using Terbium probe
definition source: RNA ontology

feature extraction
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has specified input
  some values from: image
subclass of: Restriction
  on property: has specified output
  some values from: data item
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200005
editor preferred term: feature extraction
has curation status: IAO_0000123
definition: A planed process with objective of obtaining quantified values from an image.
term editor: PERSON: Jie Zheng
definition source: MO_928: feature_extraction

OH-radical structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: OH-radical structure mapping assay
example of usage: PMID:2501870
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe
term editor: Philippe Rocca-Serra
alternative label: MOHCA assay
alternative label: OH footprinting assay
alternative label: single nucleotide resolution mapping assay using OH-radical probe
definition source: RNA ontology

RNASE T1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000025467
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025467
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: RNASE T1 structure mapping assay
example of usage: PMID:114514
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using RNAse T1
definition source: RNA ontology

array image creation
type: Class
subclass of: image creation
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0400147
subclass of: Restriction
  on property: has specified output
  some values from: image
editor preferred term: array image acquisition
has curation status: IAO_0000123
definition: An image creation process that generate an image from the array.
term editor: PERSON: Jie Zheng
alternative label: array image acquisition
definition source: MO_929: image_acquisition

light emission device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: light emission function
subclass of: device
editor preferred term: light emission device
example of usage: A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
has curation status: IAO_0000120
definition: A device which has a function to emit light.
term editor: Person:Helen Parkinson
definition source: OBI

perturbation device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: perturb function
subclass of: device
editor preferred term: perturbation device
example of usage: A homogenizer is a perturbation device.
has curation status: IAO_0000123
definition: A perturbation device is a device which is designed to perform a perturb function
term editor: Helen Parkinson
definition source: OBI Vancouver workshop 2010
definition source: PERSON: Helen Parkinson

environmental control device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: Class
      union of: heat function
      union of: cool function
      union of: environment control function
subclass of: device
editor preferred term: environmental control device
example of usage: A growth chamber is an environmental control device.
has curation status: IAO_0000120
definition: An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
term editor: Helen Parkinson
definition source: OBI

Nuclease S1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000025471
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000025471
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of sequence macromolecule
editor preferred term: Nuclease S1 structure mapping assay
example of usage: PMID:363143
has curation status: IAO_0000122
definition: A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe.
term editor: Philippe Rocca-Serra
alternative label: single nucleotide resolution mapping assay using Nuclease S1
definition source: RNA ontology

specimen fixation function
type: Class
subclass of: function
editor preferred term: specimen fixation function
example of usage: e.g the function of a bar code reader used to read slide bar codes
has curation status: IAO_0000123
definition: a function that allows specific identification of individual speciment from one another.
term editor: EAGLE-I

obsolete_specimen fixation function
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_specimen fixation function
has curation status: IAO_0000123
definition: A specimen fixation function is a function that holds or fastens an entity in a fixed position.
term editor: EAGLE-I
has obsolescence reason: IAO_0000227
deprecated: true

Ruthenium structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: Ruthenium structure mapping assay
example of usage: PMID:3016894
has curation status: IAO_0000122
definition: A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe
term editor: Philippe Rocca-Serra
definition source: RNA Ontology

inline probing RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: measurement datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: secondary structure of RNA molecule
editor preferred term: inline probing RNA structure mapping assay
example of usage: PMID:10573122 and PMID: 18369975
has curation status: IAO_0000122
definition: A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity
term editor: Philippe Rocca-Serra
definition source: RNA ontology

current amplification function
type: Class
subclass of: function
editor preferred term: current amplification function
has curation status: IAO_0000123
definition: A current amplification function is an amplification function that increases the amplitude of a current.
term editor: EAGLE-I

stabilization function
type: Class
subclass of: function
editor preferred term: stabilization function
has curation status: IAO_0000123
definition: 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.
term editor: EAGLE-I
alternative label: isolation function

pump function
type: Class
subclass of: transfer function
editor preferred term: pump function
has curation status: IAO_0000123
definition: a transfer unction where the transfer requires work to move the entity, often against a gradient.
term editor: EAGLE-I

cell transfer function
type: Class
subclass of: transfer function
editor preferred term: cell transfer function
example of usage: A cell harvester has a cell transfer function.
has curation status: IAO_0000123
definition: is a transfer function that displaces cells from one place to another
term editor: EAGLE-I

angiograph
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: record function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: angiograph
has curation status: IAO_0000120
definition: A device that records the patterns of pulse waves inside blood vessels.
term editor: PERSON: Erik Segerdell
definition source: http://medical-dictionary.thefreedictionary.com/angiograph

capillary blotter
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: capillary blotter
has curation status: IAO_0000120
definition: A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed.
term editor: PERSON: Erik Segerdell
definition source: http://www.biometra.de/

bioreactor
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: bioreactor
has curation status: IAO_0000120
definition: A device or system that supports a biologically active environment.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Bioreactor

pH meter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: pH meter
has curation status: IAO_0000120
definition: A device that is used to measure the pH (acidity or alkalinity) of a liquid.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/PH_meter

digital camera
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
editor preferred term: digital camera
has curation status: IAO_0000120
definition: An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Digital_camera

chip spotting device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred term: chip spotting device
has curation status: IAO_0000120
definition: A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 7416705

RNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
editor preferred term: RNA extraction/purification instrument
has curation status: IAO_0000120
definition: A device that is used to isolate and collect RNA for subsequent molecular analysis.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

DNA extract
type: Class
equivalent class: Class
  intersection of: nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: DNA extraction
  intersection of: Restriction
    on property: has grain
    some values from: deoxyribonucleic acid
subclass of: nucleic acid extract
editor preferred term: DNA extract
has curation status: IAO_0000120
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
term editor: Person: Jie Zheng
definition source: Group: UPenn group

two-photon laser/detector
type: Class
subclass of: OBI_0400065
editor preferred term: two-photon laser/detector
has curation status: IAO_0000120
definition: A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy

electrophoresis system
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
editor preferred term: electrophoresis system
has curation status: IAO_0000120
definition: A device that moves charged particles through a medium by using an electric field induced by electrodes.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Category:Electrophoresis

PET synthesizer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: synthesizing function
editor preferred term: PET synthesizer
has curation status: IAO_0000120
definition: A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

spinning-disk confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: spinning-disk confocal microscope
has curation status: IAO_0000120
definition: A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Nipkow_disk

DNA synthesizer
type: Class
subclass of: OBI_0400113
editor preferred term: DNA synthesizer
has curation status: IAO_0000120
definition: An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
term editor: PERSON: Erik Segerdell
definition source: http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers

high performance liquid chromatography instrument
type: Class
subclass of: liquid chromatography instrument
editor preferred term: high performance liquid chromatography instrument
has curation status: IAO_0000120
definition: A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/High_performance_liquid_chromatography

microplate reader
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: microplate reader
has curation status: IAO_0000120
definition: A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Plate_reader

ELISA microplate reader
type: Class
subclass of: microplate reader
editor preferred term: ELISA microplate reader
has curation status: IAO_0000120
definition: A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

spot cutter
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: spot cutter
has curation status: IAO_0000120
definition: A robotic device that is used to excise spots from gels.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

microwave synthesis system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: excitation function
subclass of: Restriction
  on property: has function
  some values from: synthesizing function
editor preferred term: microwave synthesis system
has curation status: IAO_0000120
definition: A device that is used to apply microwave irradiation to chemical reactions.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Microwave_chemistry

densitometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: densitometer
has curation status: IAO_0000120
definition: A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Densitometer

automatic staining machine
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: addition of molecular tracer function
editor preferred term: automatic staining machine
has curation status: IAO_0000120
definition: A device that is used to automatically stain tissue sections on slides or tissue specimens.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

automatic tissue processor
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: reagent application function
editor preferred term: automatic tissue processor
has curation status: IAO_0000120
definition: A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 3762362

stereo microscope
type: Class
subclass of: optical microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: stereo microscope
has curation status: IAO_0000120
definition: An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope

top loading balance
type: Class
subclass of: balance
editor preferred term: top loading balance
has curation status: IAO_0000120
definition: A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

perfusion station
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: specimen fixation function
editor preferred term: perfusion station
has curation status: IAO_0000120
definition: A device or system in which perfusion units are integrated.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

SPECT scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: SPECT scanner
has curation status: IAO_0000120
definition: A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography

array manufacturer role
type: Class
subclass of: manufacturer role
subclass of: Restriction
  on property: realized in
  all values from: Class
    intersection of: manufacturing
    intersection of: Restriction
      on property: has specified output
      some values from: OBI_0400147
editor preferred term: array manufacturer role
has curation status: IAO_0000120
definition: a manufacturer role which is played by the person or organization that manufactured the array
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_695 array_manufacturer

scintillation counter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: scintillation counter
has curation status: IAO_0000120
definition: A device that is used to measure ionizing radiation.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Scintillation_counter

programmable array microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: programmable array microscope
has curation status: IAO_0000120
definition: A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
term editor: PERSON: Erik Segerdell
definition source: Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8

cryostat
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: cool function
editor preferred term: cryostat
has curation status: IAO_0000120
definition: A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Cryostat

microtome knife maker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: microtome knife maker
has curation status: IAO_0000120
definition: A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

cryofixation device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: specimen fixation function
editor preferred term: cryofixation device
has curation status: IAO_0000120
definition: A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Cryofixation

hybridization oven
type: Class
subclass of: incubator
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: hybridization oven
has curation status: IAO_0000120
definition: A device that creates an appropriate environment for nucleic acid hybridization.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

incubator shaker
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred term: incubator shaker
has curation status: IAO_0000120
definition: An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

small-animal image acquisition device
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: small-animal image acquisition device
has curation status: IAO_0000120
definition: A device that is used to image small laboratory animals (e.g., rats and mice) in vivo.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

infrared image acquisition device
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: infrared image acquisition device
has curation status: IAO_0000120
definition: An image acquisition device that is responsive to an infrared emissive target within a given field of view.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 4107530

confocal microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: confocal microscope
has curation status: IAO_0000120
definition: A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Confocal_microscopy

patch clamp device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: patch clamp device
has curation status: IAO_0000120
definition: A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Patch_clamp

gel imaging system
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: gel imaging system
has curation status: IAO_0000120
definition: A device that is used to acquire images of laboratory gels.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

protein separation apparatus
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
editor preferred term: protein separation apparatus
has curation status: IAO_0000120
definition: A device that is used for the separation of proteins.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

multichannel electronic pipette
type: Class
subclass of: multichannel pipette
editor preferred term: multichannel electronic pipette
has curation status: IAO_0000120
definition: A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations.
term editor: PERSON: Erik Segerdell
definition source: http://www.faqs.org/patents/app/20090196797

vitrification apparatus
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: vitrification apparatus
has curation status: IAO_0000120
definition: A device that is used to effect the transition of a substance into a glass.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Glass_transition

radiography instrument
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: radiography instrument
has curation status: IAO_0000120
definition: An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Medical_radiography

radiation measurement device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: record function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: radiation measurement device
has curation status: IAO_0000120
definition: A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

lyophilizer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: freeze function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: lyophilizer
has curation status: IAO_0000120
definition: A device that is used to freeze dry material.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Freeze_drying

tandem mass spectrometer
type: Class
subclass of: mass spectrometer
editor preferred term: tandem mass spectrometer
has curation status: IAO_0000120
definition: A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge.
term editor: PERSON: Erik Segerdell
definition source: http://goldbook.iupac.org/T06250.html

microhardness tester
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: microhardness tester
has curation status: IAO_0000120
definition: A hardness testing device that is used in light-optical microscopes.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 4611487

multimode microplate reader
type: Class
subclass of: microplate reader
editor preferred term: multimode microplate reader
has curation status: IAO_0000120
definition: A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

mechanical balance
type: Class
subclass of: balance
editor preferred term: mechanical balance
has curation status: IAO_0000120
definition: A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
term editor: PERSON: Erik Segerdell
definition source: http://www.britannica.com/EBchecked/topic/49765/balance

computer cluster
type: Class
subclass of: OBI_0400107
editor preferred term: computer cluster
has curation status: IAO_0000120
definition: A group of linked computers, working together closely so that in many respects they form a single computer.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Cluster_(computing)

microtome knife sharpener
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: microtome knife sharpener
has curation status: IAO_0000120
definition: A device that is used to sharpen knives used in microtomy.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

plate shaker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: plate shaker
has curation status: IAO_0000120
definition: A device that provides shaking motion for microplates.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

coagulation analyzer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: coagulation analyzer
has curation status: IAO_0000120
definition: A device for automatically analyzing blood coagulation in a clinical laboratory.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 5439646

laser capture microdissection microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: laser capture microdissection microscope
has curation status: IAO_0000120
definition: A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
term editor: PERSON: Erik Segerdell
definition source: http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine

liquid extraction robot
type: Class
subclass of: OBI_0400112
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: liquid extraction robot
has curation status: IAO_0000120
definition: A liquid handling device that provides automatic liquid extraction.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

ultrasound machine
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: ultrasound machine
has curation status: IAO_0000120
definition: A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Sonography

immunoblot scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: immunoblot scanner
has curation status: IAO_0000120
definition: A device that is used for the imaging of immunoblots.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

microcentrifuge
type: Class
subclass of: OBI_0400106
editor preferred term: microcentrifuge
has curation status: IAO_0000120
definition: A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge

electronic repeater pipette
type: Class
subclass of: micropipette
editor preferred term: electronic repeater pipette
has curation status: IAO_0000120
definition: A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
term editor: PERSON: Erik Segerdell
definition source: http://www.faqs.org/patents/app/20090196797

electron paramagnetic resonance spectrometer
type: Class
subclass of: OBI_0400115
editor preferred term: electron paramagnetic resonance spectrometer
has curation status: IAO_0000120
definition: An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance

rocker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: rocker
has curation status: IAO_0000120
definition: A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

analytical balance
type: Class
subclass of: balance
editor preferred term: analytical balance
has curation status: IAO_0000120
definition: A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Weighing_scale

scanning force microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: scanning force microscope
has curation status: IAO_0000120
definition: A microscope that forms images of surfaces using a physical probe that scans the specimen.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Scanning_probe_microscopy

pulsed-field gel electrophoresis system
type: Class
subclass of: gel electrophoresis system
editor preferred term: pulsed-field gel electrophoresis system
has curation status: IAO_0000120
definition: A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis

tissue embedding station
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: tissue embedding station
has curation status: IAO_0000120
definition: A device that is used to perform paraffin embedding of tissue specimens.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

nucleic acid sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: nucleic acid sequencer
has curation status: IAO_0000120
definition: An device that is used to determine the order of nucleotides in nucleic acid sequences.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

bead array reader
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: bead array reader
has curation status: IAO_0000120
definition: A device that is used to acquire and image bead array data.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

real-time PCR machine
type: Class
subclass of: PCR instrument
editor preferred term: real-time PCR machine
has curation status: IAO_0000120
definition: An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

paraffin oven
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: heat function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: paraffin oven
has curation status: IAO_0000120
definition: A device that is used for the warming of paraffin embedding medium.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

autoclave
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: heat function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: sterilization function
editor preferred term: autoclave
has curation status: IAO_0000120
definition: A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents.
term editor: PERSON: Erik Segerdell
definition source: J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave

microplate washer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: microplate washer
has curation status: IAO_0000120
definition: A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
term editor: PERSON: Erik Segerdell
definition source: http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037

nucleic acid extraction/purification instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
editor preferred term: nucleic acid extraction/purification instrument
has curation status: IAO_0000120
definition: A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

ELISA microplate washer
type: Class
subclass of: microplate washer
editor preferred term: ELISA microplate washer
has curation status: IAO_0000120
definition: A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

vacuum manifold
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: vacuum manifold
has curation status: IAO_0000120
definition: A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

DNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
editor preferred term: DNA extraction/purification instrument
has curation status: IAO_0000120
definition: A device that is used to isolate and collect DNA for subsequent molecular analysis.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/DNA_extraction

multichannel pipette
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: multichannel pipette
has curation status: IAO_0000120
definition: A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

cell harvester
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: cell transfer function
editor preferred term: cell harvester
has curation status: IAO_0000120
definition: A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

portable fluorometer
type: Class
subclass of: OBI_0400143
editor preferred term: portable fluorometer
has curation status: IAO_0000120
definition: A compact fluorometer that can be carried or moved with ease.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

gel electrophoresis system
type: Class
subclass of: electrophoresis system
editor preferred term: gel electrophoresis system
has curation status: IAO_0000120
definition: An electrophoresis system in which an electric field is applied to a gel matrix
term editor: PERSON: Erik Segerdell
definition source: https://en.wikipedia.org/wiki/Gel_electrophoresis

diffractometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: diffractometer
has curation status: IAO_0000120
definition: A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Diffractometer

microdissection instrument
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: microdissection instrument
has curation status: IAO_0000120
definition: A device that is used for the dissection of tissues under magnification.
term editor: PERSON: Erik Segerdell
definition source: http://medical-dictionary.thefreedictionary.com/microdissection

micropipette puller
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: micropipette puller
has curation status: IAO_0000120
definition: A device that is used to fabricate glass micropipettes.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Micropipette

laser scanning confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: laser scanning confocal microscope
has curation status: IAO_0000120
definition: A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy

digital microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: digital microscope
has curation status: IAO_0000120
definition: A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Digital_microscope

freeze substitution system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: freeze function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: freeze substitution system
has curation status: IAO_0000120
definition: A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
term editor: PERSON: Erik Segerdell
definition source: doi:10.1017/S143192760707866X

micropipette
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: micropipette
has curation status: IAO_0000120
definition: A microinjection device that is used to measure very small volumes of liquids.
term editor: PERSON: Erik Segerdell
definition source: http://www.answers.com/topic/micropipette

voltage clamp device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: voltage clamp device
has curation status: IAO_0000120
definition: A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Voltage_clamp

vacuum oven
type: Class
subclass of: container
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: heat function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred term: vacuum oven
has curation status: IAO_0000120
definition: A device that heats materials in a vacuum.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

slide warmer
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: heat function
editor preferred term: slide warmer
has curation status: IAO_0000120
definition: A device that is used to heat microscope slides.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

capillary electrophoresis instrument
type: Class
subclass of: electrophoresis system
editor preferred term: capillary electrophoresis instrument
has curation status: IAO_0000120
definition: An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Capillary_electrophoresis

denaturing high-performance liquid chromatography instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
editor preferred term: denaturing high-performance liquid chromatography instrument
has curation status: IAO_0000120
definition: A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis.
term editor: PERSON: Erik Segerdell
definition source: doi:10.1385/1-59259-850-1:173

agarose gel electrophoresis system
type: Class
subclass of: gel electrophoresis system
editor preferred term: agarose gel electrophoresis system
has curation status: IAO_0000120
definition: A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis

balance
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: balance
has curation status: IAO_0000120
definition: A measuring instrument that is used to determine the weight or mass of an object.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Weighing_scale

surface plasmon resonance instrument
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: surface plasmon resonance instrument
has curation status: IAO_0000120
definition: A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Surface_plasmon_resonance

protein sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred term: protein sequencer
has curation status: IAO_0000120
definition: An device that is used to determine the order of amino acids in protein sequences.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell

X-ray source
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: excitation function
editor preferred term: X-ray source
has curation status: IAO_0000120
definition: A device that is used to generate X-rays.
term editor: PERSON: Erik Segerdell
alternative label: x-ray generator
definition source: http://en.wikipedia.org/wiki/X-ray_generator

liquid chromatography instrument
type: Class
subclass of: chromatography device
editor preferred term: liquid chromatography instrument
has curation status: IAO_0000120
definition: A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush

spike-in quality control role
type: Class
subclass of: reference substance role
editor preferred term: spike-in quality control role
has curation status: IAO_0000120
definition: a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
term editor: PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
definition source: MO_937 spike_quality_control

individual organism identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: OBI_0100026
editor preferred term: individual organism identifier
has curation status: IAO_0000120
definition: a CRID symbol used to distinguish one individual organism from another.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_169 Individual

dye swap quality control role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: characteristic of
  some values from: labeled nucleic acid extract
editor preferred term: dye swap quality control role
has curation status: IAO_0000120
definition: a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_524 dye_swap_quality_control

labeled nucleic acid extract
type: Class
equivalent class: Class
  intersection of: labeled specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: OBI_0600038
      intersection of: Restriction
        on property: has specified input
        some values from: nucleic acid extract
  intersection of: Restriction
    on property: has grain
    some values from: nucleic acid
subclass of: labeled specimen
editor preferred term: labeled nucleic acid extract
has curation status: IAO_0000120
definition: 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.
term editor: Person: Jie Zheng
alternative label: labeled extract
definition source: MO_221 labeledExtract

binding constant
type: Class
subclass of: OBI_0003142
editor preferred term: binding constant
example of usage: The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
has curation status: IAO_0000123
definition: A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed.
editor note: 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class.
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum

3D structure determination of bound molecular complex assay
type: Class
equivalent class: Class
  intersection of: OBI_0003117
  intersection of: Restriction
    on property: has specified output
    some values from: 3D structural organization datum
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: complex of molecules
subclass of: OBI_0003117
editor preferred term: 3D structure determination of bound molecular complex assay
example of usage: Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
has curation status: IAO_0000120
definition: A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration.
term editor: IEDB
definition source: IEDB

binding assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: binding datum
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: OBI_0001588
editor preferred term: binding assay
example of usage: Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
has curation status: IAO_0000123
definition: An assay with the objective to characterize the disposition of two or more material entities to form a complex.
term editor: Bjoern Peters
term editor: Jason Greenbaum
term editor: Randi Vita

cell culture expansion
type: Class
subclass of: material processing
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0100060
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0100060
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: cell culture expansion
has curation status: IAO_0000120
definition: a process that results in the increase of cell numbers
editor note: including grow of yeast and bacteria
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_758 grow
curator note: BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.

gene knock out
type: Class
subclass of: OBI_0600043
editor preferred term: gene knock out
has curation status: IAO_0000120
definition: a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_771 gene_knock_out

gene knock in
type: Class
subclass of: OBI_0600043
editor preferred term: gene knock in
has curation status: IAO_0000120
definition: a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_437 gene_knock_in
definition source: WEB: http://en.wikipedia.org/wiki/Gene_Knock-in

chromosomal substitution
type: Class
subclass of: OBI_0600043
editor preferred term: chromosomal substitution
has curation status: IAO_0000120
definition: A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_995 chromosomal_substitution

genetically modified material
type: Class
equivalent class: Class
  union of: OBI_0302859
  union of: Class
    intersection of: cell
    intersection of: Restriction
      on property: is specified output of
      some values from: OBI_0600043
subclass of: processed material
editor preferred term: genetically modified material
has curation status: IAO_0000120
definition: a material entity, organism or cell, that is the output of a genetic transformation process.
term editor: PERSON: Jie Zheng
definition source: GROUP: OBI
curator note: term is proposed by BP on Oct 25, 2010 dev call

transfection
type: Class
subclass of: OBI_0600043
subclass of: Restriction
  on property: has part
  some values from: OBI_0600033
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: Class
      union of: deoxyribonucleic acid
      union of: ribonucleic acid
    intersection of: Restriction
      on property: has characteristic
      some values from: target of material addition role
editor preferred term: transfection
has curation status: IAO_0000120
definition: a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_366 transfection

genetic transformation objective
type: Class
subclass of: material transformation objective
editor preferred term: genetic transformation objective
has curation status: IAO_0000120
definition: a material transformation objective aims to create genetically modified organism or cell
term editor: Person: Jie Zheng
definition source: Person: Jie Zheng
curator note: suggested to be added by BP and AR during Oct 25, 2010 dev call

induced mutagenesis
type: Class
subclass of: OBI_0600043
editor preferred term: induced mutagenesis
has curation status: IAO_0000120
definition: A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation.
editor note: Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_564 induced_mutation

3D structural organization datum
type: Class
subclass of: measurement datum
editor preferred term: 3D structural organization datum
example of usage: The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
has curation status: IAO_0000123
definition: A measurement datum that describes the structural orientation of a material entity in 3D space.
term editor: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters

age since planting measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since planting measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_495 planting
curator note: Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call

age since hatching measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since hatching measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_745 hatching

age determination assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: OBI_0100026
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_0100026
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has specified output
  some values from: age measurement datum
editor preferred term: age determination assay
has curation status: IAO_0000120
definition: An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted).
editor note: This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
term editor: Alan Ruttenberg
alternative label: age measurement assay
definition source: OBI group

age since egg laying measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since egg laying measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_767 egg laying

assay validation objective
type: Class
subclass of: objective specification
editor preferred term: assay validation objective
has curation status: IAO_0000120
definition: an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: GROUP: Penn Group

age since germination measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since germination measurement datum
has curation status: IAO_0000120
definition: 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.
editor note: Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_590 germination

validation by reverse transcription PCR design
type: Class
subclass of: OBI_0500000
editor preferred term: validation by reverse transcription PCR design
has curation status: IAO_0000120
definition: a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_986 reverse_transcription_PCR_quality_control

age since eclosion measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since eclosion measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_876 eclosion

age since sowing measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since sowing measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_748 sowing

age since coitus measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since coitus measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_783 coitus

validation by real time PCR design
type: Class
subclass of: OBI_0500000
editor preferred term: validation by real time PCR design
has curation status: IAO_0000120
definition: a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_434 real_time_PCR_quality_control

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0000011
editor preferred term: age measurement datum
has curation status: IAO_0000120
definition: A time measurement datum that is the result of measurement of age of an organism
editor note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage.
term editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
curator note: In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.

age since fertilization measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since fertilization measurement datum
has curation status: IAO_0000120
definition: 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.
editor note: Definition of fertilization comes from GO.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_701 fertilization

age since birth measurement datum
type: Class
subclass of: age measurement datum
editor preferred term: age since birth measurement datum
has curation status: IAO_0000120
definition: 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.
term editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_710 birth

reverse transcription polymerase chain reaction assay
type: Class
subclass of: OBI_0002692
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: RNA extract
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: RNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has part
  some values from: reverse transcribed polymerase chain reaction
subclass of: Restriction
  on property: has specified input
  some values from: RNA extract
subclass of: Restriction
  on property: has specified output
  some values from: information content entity
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: gene expression
editor preferred term: reverse transcription polymerase chain reaction assay
has curation status: IAO_0000120
definition: An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
term editor: Chris Stoeckert
term editor: Jie Zheng
definition source: Penn Group

half life datum (t 1/2)
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000003
editor preferred term: half life datum (t 1/2)
has curation status: IAO_0000120
definition: The time it takes for 50% of a class of stochastic processes to occur.
term editor: Bjoern Peters
alternative label: t 1/2
definition source: Bjoern Peters

dose response curve
type: Class
subclass of: line graph
editor preferred term: dose response curve
has curation status: IAO_0000120
definition: 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.
term editor: Bjoern Peters; Randi Vita

service
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: service consumer role
    intersection of: Restriction
      on property: realizes
      some values from: service provider role
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: planned process
editor preferred term: service
example of usage: 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.
has curation status: IAO_0000120
definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
term editor: Carlo; Matt
definition source: OBI workshop San Diego 2011

passive immunization
type: Class
subclass of: OBI_0600007
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: material to be added role
    intersection of: Restriction
      on property: role of
      some values from: OBI_1110022
editor preferred term: passive immunization
example of usage: Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another.
has curation status: IAO_0000123
definition: The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens.
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
alternative label: adoptive transfer

selective organism creation objective
type: Class
subclass of: objective specification
editor preferred term: selective organism creation objective
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29

Individual epitope immunization in vivo
type: Class
subclass of: OBI_1110015
editor preferred term: Individual epitope immunization in vivo
example of usage: Injection of a peptide T cell epitope into a mouse
has curation status: IAO_0000120
definition: An immunization in which an individual epitope is administered into a host organism.
editor note: 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.
term editor: PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita

RNA sequencing assay
type: Class
equivalent class: Class
  intersection of: OBI_0600047
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400103
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: Class
        intersection of: RNA extract
        intersection of: Restriction
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600028
  intersection of: Restriction
    on property: has specified input
    some values from: RNA extract
  intersection of: Restriction
    on property: has specified output
    some values from: sequence data
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: primary structure of RNA molecule
subclass of: OBI_0600047
editor preferred term: RNA sequencing assay
has curation status: IAO_0000120
definition: An assay that determines the sequence of an RNA molecule.
term editor: Bjoern Peters
definition source: Bjoern Peters

efficacy of epitope intervention experiment
type: Class
subclass of: assay
editor preferred term: efficacy of epitope intervention experiment
has curation status: IAO_0000120
definition: An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism.
term editor: Bjoern Peters
alternative label: efficacy of in vivo intervention

epitope protection from infectious challenge experiment
type: Class
subclass of: epitope protection experiment
editor preferred term: epitope protection from infectious challenge experiment
has curation status: IAO_0000120
definition: An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
term editor: Bjoern Peters
alternative label: protection from infectious challenge

half maximal effective concentration (EC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
editor preferred term: half maximal effective concentration (EC50)
example of usage: 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.
has curation status: IAO_0000120
definition: 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.
term editor: Bjoern Peters; Randi Vita
definition source: wikipedia

binding datum
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: OBI_0001588
subclass of: data item
editor preferred term: binding datum
has curation status: IAO_0000120
definition: 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.
term editor: Bjoern Peters; Randi Vita

negative binding datum
type: Class
subclass of: OBI_0003141
editor preferred term: negative binding datum
has curation status: IAO_0000123
definition: A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex.

epitope protection from tumor challenge experiment
type: Class
subclass of: epitope protection experiment
editor preferred term: epitope protection from tumor challenge experiment
has curation status: IAO_0000120
definition: An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
term editor: Bjoern Peters
alternative label: protection from tumor challenge

epitope protection experiment
type: Class
subclass of: efficacy of epitope intervention experiment
editor preferred term: epitope protection experiment
has curation status: IAO_0000120
definition: An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
term editor: Bjoern Peters
alternative label: protection from challenge

selectively maintained organism
type: Class
equivalent class: Class
  intersection of: OBI_0100026
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: planned process
      intersection of: Restriction
        on property: achieves_planned_objective
        some values from: selective organism creation objective
subclass of: OBI_0100026
editor preferred term: selectively maintained organism
has curation status: IAO_0000120
definition: An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
term editor: Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
alternative label: cultivar
alternative label: ecotype
alternative label: strain
definition source: MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar

epitope protection from infectious challenge experiment based on pathogen burden
type: Class
subclass of: epitope protection from infectious challenge experiment
editor preferred term: epitope protection from infectious challenge experiment based on pathogen burden
has curation status: IAO_0000120
definition: An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls.
term editor: Bjoern Peters
alternative label: burden after infectious challenge

infectious agent detection assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: infection
editor preferred term: infectious agent detection assay
example of usage: Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus.
has curation status: IAO_0000120
definition: An assay that measures the presence or amount of an infectious agent in an evaluant
term editor: Bjoern Peters
term editor: Jason Greenbaum
term editor: Randi Vita
term editor: Richard Scheuermann

epitope disease exacerbation experiment
type: Class
subclass of: efficacy of epitope intervention experiment
editor preferred term: epitope disease exacerbation experiment
has curation status: IAO_0000120
definition: An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
term editor: Bjoern Peters
alternative label: exacerbation assay

epitope protection experiment based on survival
type: Class
subclass of: epitope protection experiment
editor preferred term: epitope protection experiment based on survival
has curation status: IAO_0000120
definition: An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
term editor: Bjoern Peters
alternative label: host survival after challenge

epitope treatment experiment
type: Class
subclass of: efficacy of epitope intervention experiment
editor preferred term: epitope treatment experiment
has curation status: IAO_0000120
definition: An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
term editor: Bjoern Peters
alternative label: decreased disease symptoms after treatment

half maximal inhibitory concentration (IC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
editor preferred term: half maximal inhibitory concentration (IC50)
example of usage: Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
has curation status: IAO_0000120
definition: 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.
term editor: Bjoern Peters; Randi Vita
definition source: wikipedia

epitope specific immune intervention
type: Class
subclass of: passive immunization
subclass of: Class
  union of: passive immunization
  union of: Individual epitope immunization in vivo
editor preferred term: epitope specific immune intervention
has curation status: IAO_0000120
definition: An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
term editor: Person: Bjoern Peters, Randi Vita, Jason Greenbaum

epitope specific cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: cytokine production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: cytokine production
editor preferred term: epitope specific cytokine production by T cells
has curation status: IAO_0000122
definition: A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: assay measuring epitope specific transforming growth factor-beta production by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TGFb release|ELISPOT

operator variation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
editor preferred term: operator variation design
has curation status: IAO_0000120
definition: A study design that assesses the operator performance and relation to data consistency and quality.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_519 operator_variation_design

cytometric bead array assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: IP-10 production
        intersection of: Restriction
subclass of: assay measuring epitope specific IP-10 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific IP-10 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects IP-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CXCL10/IP-10 release|cytometric bead array

comparative genome hybridization by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
editor preferred term: comparative genome hybridization by array design
has curation status: IAO_0000120
definition: A study design that detects genomic copy number variations using microarray technology.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_856 comparative_genome_hybridization_design

assay measuring epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-27 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-27 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-27 release|biological activity

in vivo design
type: Class
subclass of: OBI_0500000
editor preferred term: in vivo design
has curation status: IAO_0000120
definition: A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_454 in_vivo_design

genotyping by high throughput sequencing design
type: Class
subclass of: genotyping design
editor preferred term: genotyping by high throughput sequencing design
has curation status: IAO_0000120
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_560 genotyping_design

epitope specific tolerance induction by T cells
type: Class
equivalent class: Class
  intersection of: tolerance induction
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: tolerance induction
editor preferred term: epitope specific tolerance induction by T cells
has curation status: IAO_0000122
definition: A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

innate behavior design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
editor preferred term: innate behavior design
has curation status: IAO_0000120
definition: A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_355 innate_behavior_design

detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific transforming growth factor-beta production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TGFb release|RNA/DNA detection

SNP microarray
type: Class
subclass of: OBI_0400148
editor preferred term: SNP microarray
has curation status: IAO_0000120
definition: A DNA microarray used to detect polymorphisms in DNA samples
term editor: Person: Helen Parkinson
definition source: EFO_0002703 SNP array

cell component comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: cellular feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: cellular_component
editor preferred term: cell component comparison design
has curation status: IAO_0000120
definition: A study design that compares samples from different cell components.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_1019 cell_component_comparison_design

ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte macrophage colony-stimulating factor production
        intersection of: Restriction
subclass of: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: GM-CSF release|ELISPOT

epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: macrophage inflammatory protein-1 alpha production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: macrophage inflammatory protein-1 alpha production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000122
definition: A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific T cell activation
type: Class
equivalent class: Class
  intersection of: T cell activation
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: T cell activation
editor preferred term: epitope specific T cell activation
has curation status: IAO_0000122
definition: A process of T cell activation resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-10 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-10 release|biological activity

cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: assay measuring epitope specific transforming growth factor-beta production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects transforming growth factor-beta production by T cells
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TGFb release|cytometric bead array

ex vivo design
type: Class
subclass of: OBI_0500000
editor preferred term: ex vivo design
has curation status: IAO_0000120
definition: A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_808 ex_vivo_design

epitope specific type IV hypersensitivity by T cells
type: Class
equivalent class: Class
  intersection of: type IV hypersensitivity
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: type IV hypersensitivity
editor preferred term: epitope specific type IV hypersensitivity by T cells
has curation status: IAO_0000122
definition: A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

normalization testing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: software testing objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: OBI_0200169
editor preferred term: normalization testing design
has curation status: IAO_0000120
definition: A study design that tests different normalization procedures.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_729 normalization_testing_design

intracellular material detection assay measuring epitope specific perforin release
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003317
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific perforin release by T cells
editor preferred term: intracellular material detection assay measuring epitope specific perforin release
has curation status: IAO_0000120
definition: A flow cytometry assay that detects epitope specific perforin release by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: perforin release|intracellular staining

cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-2 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-2 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-2 release|bioassay

assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-22 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-22 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-22 release|biological activity

assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-8 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-8 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-8 release|biological activity

epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: chemokine (C-C motif) ligand 1 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: chemokine (C-C motif) ligand 1 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000122
definition: A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-10 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-10 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-10 release|bioassay

ChIP-chip by SNP array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: SNP microarray
  intersection of: Restriction
    on property: has specified input
    some values from: SNP microarray
editor preferred term: ChIP-chip by SNP array assay
has curation status: IAO_0000120
definition: A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin
term editor: ArrayExpress production team
definition source: EFO:0002764

ELISA measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 5 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific RANTES production by T cells
editor preferred term: ELISA measuring epitope specific RANTES production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects RANTES production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL5/RANTES release|ELISA

cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-1 beta production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-1 beta production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-1 beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-1b release|cytometric bead array

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: part of
  some values from: genotype information
editor preferred term: genetic population background information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
has curation status: IAO_0000120
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group

environmental history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
editor preferred term: environmental history design
has curation status: IAO_0000120
definition: A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_698 environmental_history_design

ELISPOT assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-6 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-6 production by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects interleukin-6 production by T cells
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-6 release|ELISPOT

in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: helper T cell enhancement of B cell mediated immune response
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
subclass of: in vivo assay measuring epitope specific T cell helper activity
editor preferred term: in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
has curation status: IAO_0000120
definition: A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response.
term editor: IEDB
definition source: IEDB
IEDB alternative term: antibody help|in vivo assay

plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: surface plasmon resonance binding assay
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0001536
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: OBI_1110057
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: surface plasmon resonance binding assay
subclass of: OBI_0002097
editor preferred term: plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
has curation status: IAO_0000120
definition: A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: dissociation constant KD|surface plasmon resonance (SPR)|nM

assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-5 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-5 release|biological activity

ELISA measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific transforming growth factor-beta production by T cells
editor preferred term: ELISA measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TGFb release|ELISA

assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 5 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific RANTES production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects RANTES production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL5/RANTES release|biological activity

assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte macrophage colony-stimulating factor production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: GM-CSF release|biological activity

epigenetic modification identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred term: epigenetic modification identification objective
has curation status: IAO_0000120
definition: A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
term editor: Chris Stoeckert, Jie Zheng
definition source: Person: Chris Stoeckert

transcription profiling by tiling array assay
type: Class
subclass of: transcription profiling by array assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: tiling microarray
  intersection of: Restriction
    on property: has specified input
    some values from: tiling microarray
editor preferred term: transcription profiling by tiling array assay
has curation status: IAO_0000120
definition: A transcription profiling by array assay that uses a tiling path array.
term editor: James Malone
definition source: EFO:0002769

ELISA measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-22 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-22 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-22 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-22 release|ELISA

assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-21 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-21 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-21 release|biological activity

ELISA measuring epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-9 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring interleukin-9 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-9 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-9 release|ELISA

transcription profiling by high throughput sequencing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
editor preferred term: transcription profiling by high throughput sequencing design
has curation status: IAO_0000120
definition: A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: ArrayExpress production team

intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-6 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-6 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-6 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-6 release|ICS

cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-4 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-4 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-4 release|bioassay

detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor production
        intersection of: Restriction
subclass of: assay measuring epitope specific tumor necrosis factor alpha production by T cells
subclass of: OBI_0001788
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNFa release|RNA/DNA detection

cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: monocyte chemotactic protein-1 production
        intersection of: Restriction
subclass of: assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL2/MCP-1 release|cytometric bead array

ELISA measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-23 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-23 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-23 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-23 release|ELISA

detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003317
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific perforin release by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
has curation status: IAO_0000120
definition: A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: perforin release|RNA/DNA detection

ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor superfamily cytokine production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
editor preferred term: ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNF release|ELISA

genotyping by high throughput sequencing assay
type: Class
subclass of: genotyping assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
editor preferred term: genotyping by high throughput sequencing assay
has curation status: IAO_0000120
definition: A genotyping assay that uses a high througput sequencer
term editor: James Malone
definition source: EFO:0002771

ChIP-chip assay
type: Class
equivalent class: Class
  intersection of: OBI_0001954
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has specified input
      some values from: OBI_0400148
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: OBI_0001985
      intersection of: OBI_0003368
subclass of: OBI_0001954
editor preferred term: ChIP-chip assay
has curation status: IAO_0000120
definition: An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin
term editor: Bjoern Petesr
term editor: James Malone
alternative label: ChIP-on-chip assay
definition source: url:http://en.wikipedia.org/wiki/ChIP-on-chip

epitope specific T cell tolerance induction
type: Class
equivalent class: Class
  intersection of: T cell tolerance induction
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: T cell tolerance induction
subclass of: epitope specific tolerance induction by T cells
editor preferred term: epitope specific T cell tolerance induction
has curation status: IAO_0000122
definition: A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
has curation status: IAO_0000122
definition: An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
has obsolescence reason: IAO_0000227
term replaced by: flow cytometry assay
IEDB alternative term: T cell degranulation by intracellular staining
deprecated: true

assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-13 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-13 release|biological activity

array platform variation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: methodology testing objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: microarray platform
editor preferred term: array platform variation design
has curation status: IAO_0000120
definition: A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_899 array_platform_variation_design

assay measuring interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-9 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring interleukin-9 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-9 release|biological activity

epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-3 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-3 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-3 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-5 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-5 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-5 release|RNA/DNA detection

epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: lymphotoxin A production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: lymphotoxin A production
subclass of: epitope specific tumor necrosis factor superfamily cytokine production by T cells
editor preferred term: epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000122
definition: A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-1 alpha production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-1 alpha production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-1 alpha production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

ChIP-seq design
type: Class
subclass of: protein binding site identification design
subclass of: Restriction
  on property: has part
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: has part
  some values from: protein and DNA interaction identification objective
editor preferred term: ChIP-seq design
has curation status: IAO_0000120
definition: A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: http://en.wikipedia.org/wiki/Chip-Sequencing

translational bias design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
editor preferred term: translational bias design
has curation status: IAO_0000120
definition: A study design that characterizes the association of transcripts and translation machinery.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_939 translational_bias_design

ELISA measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-3 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-3 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-3 release|ELISA

ELISA measuring epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-1 alpha production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-1 alpha production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-1 alpha production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-1a release|ELISA

epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-27 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-27 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-27 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: helper T cell enhancement of T cell mediated immune response
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
subclass of: in vivo assay measuring epitope specific T cell helper activity
editor preferred term: in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
has curation status: IAO_0000120
definition: A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: T cell help|in vivo assay

assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TGFb release|biological activity

FWER adjusted p-value
type: Class
subclass of: quantitative confidence value
editor preferred term: FWER adjusted p-value
example of usage: http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
has curation status: IAO_0000122
definition: A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
term editor: PERS:Philippe Rocca-Serra
definition source: adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)

DNA methylation profiling by high throughput sequencing assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400103
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400103
editor preferred term: DNA methylation profiling by high throughput sequencing assay
has curation status: IAO_0000120
definition: A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology
term editor: ArrayExpress production team
term editor: Helen Parkinson
term editor: James Malone
definition source: EFO:0002761

epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: transforming growth factor beta production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: transforming growth factor beta production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122
definition: A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-12 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-12 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-12 release|RNA/DNA detection

assay measuring epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: Restriction
subclass of: OBI_0002055
editor preferred term: assay measuring epitope specific cytotoxic T cell degranulation
has curation status: IAO_0000120
definition: A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: degranulation|biological activity

cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific transforming growth factor-beta production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TGFb release|bioassay

RNA-seq assay
type: Class
subclass of: RNA sequencing assay
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: gene expression
editor preferred term: RNA-seq assay
has curation status: IAO_0000120
definition: An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
term editor: James Malone
alternative label: transcription profiling by high throughput sequencing
definition source: EFO:0002770

ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor superfamily cytokine production
        intersection of: Restriction
subclass of: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNF release|ELISPOT

cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-5 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-5 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-5 release|bioassay

genotyping by array assay
type: Class
subclass of: genotyping assay
subclass of: OBI_0001985
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
editor preferred term: genotyping by array assay
has curation status: IAO_0000120
definition: A genotyping assay that uses an array
term editor: ArrayExpress production team
definition source: EFO:0002767

epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-16 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-16 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-16 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 1 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL1/TCA-3 release|biological activity

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-2 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-2 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-2 release|RNA/DNA detection

DNA methylation profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: epigenetic modification identification objective
editor preferred term: DNA methylation profiling by array design
has curation status: IAO_0000120
definition: A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: GROUP: ArrayExpress production team

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-22 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-22 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-22 release|RNA/DNA detection

assay measuring epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-16 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-16 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-16 release|biological activity

ELISA measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: IP-10 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific IP-10 production by T cells
editor preferred term: ELISA measuring epitope specific IP-10 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects IP-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CXCL10/IP-10 release|ELISA

translation profiling assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
editor preferred term: translation profiling assay
has curation status: IAO_0000120
definition: An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
term editor: James Malone
definition source: EFO:0001033

ELISA measuring epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-15 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-15 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-15 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-15 release|ELISA

cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-12 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-12 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-12 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-12 release|cytometric bead array

in vitro design
type: Class
subclass of: OBI_0500000
editor preferred term: in vitro design
has curation status: IAO_0000120
definition: A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_347 in_vitro_design

RNAi profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
editor preferred term: RNAi profiling by array design
has curation status: IAO_0000120
definition: A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: ArrayExpress production team

ELISA measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: lymphotoxin A production
        intersection of: Restriction
subclass of: ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: assay measuring epitope specific lymphotoxin A production by T cells
editor preferred term: ELISA measuring epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: lymphotoxin A/TNFb release|ELISA

cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-5 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-5 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-5 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-5 release|cytometric bead array

transcription profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
editor preferred term: transcription profiling by array design
has curation status: IAO_0000120
definition: A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_533 transcript_identification_design

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-17 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-17 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-17 release|RNA/DNA detection

assay measuring epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-15 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-15 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-15 release|biological activity

disease state design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: OGMS_0000031
editor preferred term: disease state design
has curation status: IAO_0000120
definition: A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_902 disease_state_design

wild type organism genotype information
type: Class
subclass of: genotype information
editor preferred term: wild type organism genotype information
example of usage: C57BL/6J wild type
has curation status: IAO_0000120
definition: a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group

assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-17 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-17 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-17 release|biological activity

cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-17 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-17 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-17 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-17 release|cytometric bead array

cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-10 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-10 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-10 production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-10 release|cytometric bead array

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-21 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-21 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-21 release|RNA/DNA detection

intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-5 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-5 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-5 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-5 release|ICS

cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-2 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-2 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-2 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-2 release|cytometric bead array

cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-16 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-16 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-16 release|bioassay

ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: macrophage inflammatory protein-1 alpha production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
editor preferred term: ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL3/MIP-1a release|ELISA

intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte macrophage colony-stimulating factor production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: GM-CSF release|ICS

RNAi profiling by array assay
type: Class
subclass of: OBI_0001985
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: ribonucleic acid
  intersection of: Restriction
    on property: has specified input
    some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
editor preferred term: RNAi profiling by array assay
has curation status: IAO_0000120
definition: An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
term editor: James Malone
definition source: EFO:0001030

genotype information
type: Class
subclass of: genetic characteristics information
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: genetic population background information
  intersection of: Restriction
    on property: has part
    some values from: genetic alteration information
editor preferred term: genotype information
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
has curation status: IAO_0000120
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group

RNA stability design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: molecular feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: ribonucleic acid
editor preferred term: RNA stability design
has curation status: IAO_0000120
definition: A study design that examines the stability and/or decay of RNA transcripts.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_553 RNA_stability_design

tiling microarray
type: Class
subclass of: OBI_0400148
editor preferred term: tiling microarray
has curation status: IAO_0000120
definition: A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
term editor: Person: Helen Parkinson
alternative label: genome tiling array
definition source: EFO_0002704: tiling array

assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: IP-10 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific IP-10 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects IP-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CXCL10/IP-10 release|biological activity

intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-13 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-13 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-13 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-13 release|ICS

species comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: OBI_0100026
editor preferred term: species comparison design
has curation status: IAO_0000120
definition: A study design that assays differences between distinct species.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_675 species_design

X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: X-ray crystallography 3D molecular structure determination assay
  intersection of: Restriction
    on property: has specified output
    some values from: 3D structural organization datum
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: OBI_0003120
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000019
subclass of: X-ray crystallography 3D molecular structure determination assay
subclass of: OBI_0001999
editor preferred term: X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
has curation status: IAO_0000120
definition: A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: 3D structure|x-ray crystallography|angstroms

transcription profiling by RT-PCR design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
editor preferred term: transcription profiling by RT-PCR design
has curation status: IAO_0000120
definition: A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: ArrayExpress production team

epitope specific T cell enhancement of B cell mediated immune response
type: Class
equivalent class: Class
  intersection of: helper T cell enhancement of B cell mediated immune response
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: helper T cell enhancement of B cell mediated immune response
editor preferred term: epitope specific T cell enhancement of B cell mediated immune response
has curation status: IAO_0000122
definition: A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 1 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
editor preferred term: ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL1/TCA-3 release|ELISA

epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-21 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-21 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-21 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
type: Class
subclass of: flow cytometry assay
subclass of: OBI_1110124
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: OBI_1110057
editor preferred term: flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
has curation status: IAO_0000120
definition: A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: T cell- APC binding|binding assay

proteomic profiling by array assay
type: Class
subclass of: OBI_0001985
subclass of: OBI_2100023
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400149
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400149
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: PR_000000001
  intersection of: Restriction
    on property: has specified input
    some values from: PR_000000001
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: PR_000000001
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
editor preferred term: proteomic profiling by array assay
has curation status: IAO_0000120
definition: An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology.
term editor: James Malone
definition source: EFO:0002765

cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: type II interferon production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interferon-gamma production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNg release|bioassay

ELISPOT assay measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
subclass of: assay measuring epitope specific granzyme B release by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific granzyme B release by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: granzyme B release|ELISPOT

microRNA profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
editor preferred term: microRNA profiling by array design
has curation status: IAO_0000120
definition: A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: ArrayExpress production team

in vivo assay measuring T cell epitope specific tolerance induction
type: Class
equivalent class: Class
  intersection of: epitope tolerance induction experiment
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: T cell tolerance induction
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
subclass of: assay measuring T cell epitope specific in vivo activity
subclass of: epitope tolerance induction experiment
editor preferred term: in vivo assay measuring T cell epitope specific tolerance induction
has curation status: IAO_0000120
definition: An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: tolerance|in vivo assay

detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 5 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific RANTES production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: CCL5/RANTES release|RNA/DNA detection

cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-4 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-4 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-4 production by T cells
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-4 release|cytometric bead array

assay measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: lymphotoxin A production
        intersection of: Restriction
subclass of: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
editor preferred term: assay measuring epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: lymphotoxin A/TNFb release|biological activity

organism development design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: UBERON_0000105
        intersection of: Restriction
editor preferred term: organism development design
has curation status: IAO_0000120
definition: A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_892 development_or_differentiation_design

family history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
editor preferred term: family history design
has curation status: IAO_0000120
definition: A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_544 family_history_design

ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-X-C motif) ligand 9 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
editor preferred term: ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: CXCL9/MIG release|ELISA

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred term: transcription profiling identification objective
has curation status: IAO_0000120
definition: A molecular feature identification objective that aims to characterize the abundance of transcripts
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: Penn Group

DNA methylation profiling by array assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
editor preferred term: DNA methylation profiling by array assay
has curation status: IAO_0000120
definition: A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology
term editor: James Malone
definition source: EFO:0002759

assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: macrophage inflammatory protein-1 alpha production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL3/MIP-1a release|biological activity

epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: granulocyte colony-stimulating factor production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: granulocyte colony-stimulating factor production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific granulocyte colony stimulating factor production by T cells
has curation status: IAO_0000122
definition: A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

microRNA profiling by array assay
type: Class
subclass of: OBI_0001926
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: ribonucleic acid
  intersection of: Restriction
    on property: has specified input
    some values from: ribonucleic acid
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: measured expression level
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: SO_0000276
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
editor preferred term: microRNA profiling by array assay
has curation status: IAO_0000120
definition: An assay that analyses the microRNA component of the transcriptome using a microRNA array.
term editor: James Malone
definition source: EFO:0000753

quality control testing design
type: Class
subclass of: OBI_0500000
editor preferred term: quality control testing design
has curation status: IAO_0000120
definition: A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_981 quality_control_testing_design

clinical history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: OGMS_0000015
editor preferred term: clinical history design
has curation status: IAO_0000120
definition: A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_832 clinical_history_design

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-4 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-4 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-4 release|RNA/DNA detection

cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte macrophage colony-stimulating factor production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: GM-CSF release|bioassay

intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-21 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-21 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-21 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-21 release|ICS

detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: monocyte chemotactic protein-1 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL2/MCP-1 release|RNA/DNA detection

ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: monocyte chemotactic protein-1 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
editor preferred term: ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL2/MCP-1 release|ELISA

assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 4 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL4/MIP-1b release|biological activity

ELISA measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-21 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-21 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-21 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-21 release|ELISA

in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
type: Class
equivalent class: Class
  intersection of: efficacy of epitope intervention experiment
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: type IV hypersensitivity
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
subclass of: efficacy of epitope intervention experiment
subclass of: assay measuring T cell epitope specific in vivo activity
editor preferred term: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
has curation status: IAO_0000120
definition: An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: type IV hypersensitivity (DTH)|in vivo skin test

cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-13 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-13 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-13 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-13 release|cytometric bead array

detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: type II interferon production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interferon-gamma production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNg release|RNA/DNA detection

epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: tumor necrosis factor superfamily cytokine production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: tumor necrosis factor superfamily cytokine production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000122
definition: A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

allele information
type: Class
subclass of: genetic alteration information
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: genotype information
  intersection of: Restriction
    on property: is about
    some values from: SO_0000001
editor preferred term: allele information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: IAO_0000120
definition: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_58 Allele

cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor production
        intersection of: Restriction
subclass of: cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: assay measuring epitope specific tumor necrosis factor alpha production by T cells
editor preferred term: cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNFa release|cytometric bead array

ELISPOT assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-17 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-17 production by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific interleukin-17 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects interleukin-17 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-17 release|ELISPOT

detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interferon-beta production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interferon-beta production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNb release|RNA/DNA detection

detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte macrophage colony-stimulating factor production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: GM-CSF release|RNA/DNA detection

post-transcriptional modification design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: study intervention
editor preferred term: post-transcriptional modification design
has curation status: IAO_0000120
definition: A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
editor note: post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_392 cellular_modification_design

ELISA measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-8 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific interleukin-8 production by T cells
editor preferred term: ELISA measuring epitope specific interleukin-8 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-8 release|ELISA

cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-6 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-6 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-6 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-6 release|cytometric bead array

transcription profiling by RT-PCR assay
type: Class
subclass of: transcription profiling assay
subclass of: OBI_0002692
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: PCR instrument
  intersection of: Restriction
    on property: has specified input
    some values from: PCR instrument
subclass of: Restriction
  on property: has part
  some values from: reverse transcribed polymerase chain reaction
editor preferred term: transcription profiling by RT-PCR assay
has curation status: IAO_0000120
definition: A transcription profiling assay that uses reverse transcription PCR (RT-PCR).
term editor: Anna Farne
definition source: EFO:0002943

epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: chemokine (C-C motif) ligand 4 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: chemokine (C-C motif) ligand 4 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000122
definition: A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-23 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-23 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-23 release|biological activity

genetic alteration information
type: Class
subclass of: genetic characteristics information
editor preferred term: genetic alteration information
has curation status: IAO_0000120
definition: a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group

cellular process design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: cellular feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: cellular process
editor preferred term: cellular process design
has curation status: IAO_0000120
definition: A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_810 cellular_process_design

epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: chemokine (C-C motif) ligand 5 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: chemokine (C-C motif) ligand 5 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific RANTES production by T cells
has curation status: IAO_0000122
definition: A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-10 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-10 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-10 release|RNA/DNA detection

cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor superfamily cytokine production
        intersection of: Restriction
subclass of: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNF release|cytometric bead array

wild type allele information
type: Class
subclass of: allele information
editor preferred term: wild type allele information
has curation status: IAO_0000120
definition: an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_605 genotype

intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 4 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL4/MIP-1b release|ICS

epitope specific granzyme B production by T cells
type: Class
equivalent class: Class
  intersection of: granzyme B production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: granzyme B production
editor preferred term: epitope specific granzyme B production by T cells
has curation status: IAO_0000122
definition: A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-8 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-8 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-8 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

injury design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
editor preferred term: injury design
has curation status: IAO_0000120
definition: A study design in which the response of an organism(s) to injury or damage is studied.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_726 injury_design

intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-3 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-3 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-3 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-3 release|ICS

organism status comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: assay
      intersection of: Restriction
        on property: has specified input
        some values from: Class
editor preferred term: organism status comparison design
has curation status: IAO_0000120
definition: A study design that compares samples from live and dead organisms.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_841 organism_status_design

ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 4 production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
editor preferred term: ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL4/MIP-1b release|ELISA

cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: type II interferon production
        intersection of: Restriction
subclass of: assay measuring epitope specific interferon-gamma production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interferon-gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNg release|cytometric bead array

assay measuring epitope specific interleukin-18 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-18 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-18 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-18 release|biological activity

epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-23 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-23 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-23 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-27 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-27 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-27 release|RNA/DNA detection

detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: IP-10 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific IP-10 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CXCL10/IP-10 release|RNA/DNA detection

cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-3 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-3 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-3 release|bioassay

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor superfamily cytokine production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNF release|ICS

epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: monocyte chemotactic protein-1 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: monocyte chemotactic protein-1 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000122
definition: A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

genotyping by array design
type: Class
subclass of: genotyping design
editor preferred term: genotyping by array design
has curation status: IAO_0000120
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_560 genotyping_design

assay measuring epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-1 alpha production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-1 alpha production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-1a release|biological activity

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-6 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-6 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-6 release|RNA/DNA detection

assay measuring epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interferon-beta production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interferon-beta production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNb release|biological activity

assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-12 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-12 release|biological activity

in vivo assay measuring epitope specific T cell killing
type: Class
equivalent class: Class
  intersection of: in vivo cell killing assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: T cell mediated cytotoxicity
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
subclass of: in vivo cell killing assay
subclass of: assay measuring T cell epitope specific in vivo activity
subclass of: OBI_1110130
editor preferred term: in vivo assay measuring epitope specific T cell killing
has curation status: IAO_0000120
definition: An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: cytotoxicity|in vivo assay

comparative genomic hybridization by array assay
type: Class
subclass of: genotyping assay
subclass of: OBI_0001985
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: characteristic of
        some values from: deoxyribonucleic acid
  intersection of: Restriction
    on property: has specified input
    some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has specified output
  some values from: genotype information
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
editor preferred term: comparative genomic hybridization by array assay
has curation status: IAO_0000120
definition: An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
term editor: James Malone
alternative label: array CGH
definition source: EFO:0000749

epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: cytotoxic T cell degranulation
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: cytotoxic T cell degranulation
editor preferred term: epitope specific cytotoxic T cell degranulation
has curation status: IAO_0000122
definition: A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: detection of specific nucleic acid polymers with complementary probes
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-23 production
        intersection of: Restriction
subclass of: detection of specific nucleic acid polymers with complementary probes
subclass of: assay measuring epitope specific interleukin-23 production by T cells
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells
has curation status: IAO_0000120
definition: A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-23 release|RNA/DNA detection

stimulus or stress design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: organism feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: response to stimulus
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: study intervention
editor preferred term: stimulus or stress design
has curation status: IAO_0000120
definition: A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_568 stimulus_or_stress_design

cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte colony-stimulating factor production
        intersection of: Restriction
subclass of: OBI_0001600
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: G-CSF release|cytometric bead array

protein and DNA interaction identification objective
type: Class
subclass of: sequence feature identification objective
editor preferred term: protein and DNA interaction identification objective
has curation status: IAO_0000120
definition: A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_933 binding_site_identification_design

epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-22 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-22 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-22 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor superfamily cytokine production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNF release|biological activity

protocol optimization design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: protocol optimization objective
editor preferred term: protocol optimization design
has curation status: IAO_0000120
definition: A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_934 optimization_design

promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: promoter activity detection by reporter gene assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-2 production
        intersection of: Restriction
subclass of: promoter activity detection by reporter gene assay
subclass of: assay measuring epitope specific interleukin-2 production by T cells
editor preferred term: promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120
definition: A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-2 release|reporter gene assay

ChIP-chip design
type: Class
subclass of: protein binding site identification design
subclass of: Restriction
  on property: has part
  some values from: protein and DNA interaction identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: immunoglobulin complex, circulating
editor preferred term: ChIP-chip design
has curation status: IAO_0000120
definition: A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
term editor: Person: Chris Stoeckert, Jie Zheng
alternative label: ChIP-on-chip design
definition source: MO_933 binding_site_identification_design

genetic characteristics information
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: SO_0000001
    intersection of: Restriction
      on property: is concretized as
      some values from: Restriction
        on property: characteristic of
        some values from: Class
editor preferred term: genetic characteristics information
has curation status: IAO_0000120
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_66 IndividualGeneticCharacteristics
curator note: MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)

cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: macrophage inflammatory protein-1 alpha production
        intersection of: Restriction
subclass of: assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL3/MIP-1a release|cytometric bead array

assay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-3 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-3 release|biological activity

assay measuring epitope specific T cell activation
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: T cell activation
        intersection of: Restriction
subclass of: OBI_0002055
editor preferred term: assay measuring epitope specific T cell activation
has curation status: IAO_0000120
definition: A T cell epitope dependent biological activity assay that detects T cell activation.
term editor: IEDB
definition source: IEDB
IEDB alternative term: activation|biological activity

imprinting design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
editor preferred term: imprinting design
has curation status: IAO_0000120
definition: A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_914 imprinting_design

cell cycle design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: cellular feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: cell cycle
editor preferred term: cell cycle design
has curation status: IAO_0000120
definition: A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_822 cell_cycle_design

translation profiling design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
editor preferred term: translation profiling design
has curation status: IAO_0000120
definition: A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: ArrayExpress production team

cell type comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: cellular feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: cell
editor preferred term: cell type comparison design
has curation status: IAO_0000120
definition: A study design that compares cells of different type, for example different cell lines.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_764 cell_type_comparison_design

cytometric bead array assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-C motif) ligand 5 production
        intersection of: Restriction
subclass of: assay measuring epitope specific RANTES production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific RANTES production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects RANTES production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL5/RANTES release|cytometric bead array

cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-6 production
        intersection of: Restriction
subclass of: reporter cell line analyte detection bioassay
subclass of: assay measuring epitope specific interleukin-6 production by T cells
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-6 release|bioassay

assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: type II interferon production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNg release|biological activity

epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-9 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-9 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-9 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

assay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor production
        intersection of: Restriction
subclass of: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
editor preferred term: assay measuring epitope specific tumor necrosis factor alpha production by T cells
has curation status: IAO_0000120
definition: An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNFa release|biological activity

ChIP-chip by tiling array design
type: Class
subclass of: ChIP-chip design
editor preferred term: ChIP-chip by tiling array design
has curation status: IAO_0000120
definition: A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: ArrayExpress production team

dose response design
type: Class
subclass of: compound treatment design
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study intervention
        intersection of: administration of material to specimen
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: dose specification
        intersection of: Restriction
editor preferred term: dose response design
has curation status: IAO_0000120
definition: A study design that examines the relationship between the size of the administered dose and the extent of the response.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_485 dose_response_design

ChIP-chip by tiling array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: tiling microarray
  intersection of: Restriction
    on property: has specified input
    some values from: tiling microarray
editor preferred term: ChIP-chip by tiling array assay
has curation status: IAO_0000120
definition: A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin
term editor: ArrayExpress production team
definition source: EFO:0002762

epitope specific helper T cell enhancement of T cell mediated immune response
type: Class
equivalent class: Class
  intersection of: helper T cell enhancement of T cell mediated immune response
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: helper T cell enhancement of T cell mediated immune response
editor preferred term: epitope specific helper T cell enhancement of T cell mediated immune response
has curation status: IAO_0000122
definition: A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: interferon-beta production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interferon-beta production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interferon-beta production by T cells
has curation status: IAO_0000122
definition: A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

organism part comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: UBERON_0000465
editor preferred term: organism part comparison design
has curation status: IAO_0000120
definition: A study design that compares tissues, regions, organs within or between organisms
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_953 organism_part_comparison_design

intracellular material detection measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific granzyme B release by T cells
editor preferred term: intracellular material detection measuring epitope specific granzyme B release by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects epitope specific granzyme B release by T cells
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: granzyme B release|intracellular staining

protein binding site identification design
type: Class
equivalent class: Restriction
  on property: has part
  some values from: protein and DNA interaction identification objective
subclass of: OBI_0500000
editor preferred term: protein binding site identification design
has curation status: IAO_0000120
definition: A study design that investigates protein binding sites on nucleic acids.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_933 binding_site_identification_design

sex comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: PATO_0000047
editor preferred term: sex comparison design
has curation status: IAO_0000120
definition: A study design that assays differences associated with an organism's sex, gender or mating type.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_575 sex_design

transcription profiling by tiling array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
editor preferred term: transcription profiling by tiling array design
has curation status: IAO_0000120
definition: A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_507 tiling_path_design

cell differentiation design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: cellular feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: cellular developmental process
editor preferred term: cell differentiation design
has curation status: IAO_0000120
definition: A study design that assays events associated with cell development or differentiation.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_892 development_or_differentiation_design

transcription profiling design
type: Class
subclass of: OBI_0500000
editor preferred term: transcription profiling design
has curation status: IAO_0000120
definition: A study design that identifies forms and abundance of transcripts in the genome.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_533 transcript_identification_design

operon identification design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: sequence feature identification objective
editor preferred term: operon identification design
has curation status: IAO_0000120
definition: A study design that identifies locations and members of operons in a genome.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_772 operon_identification_design

radio immuno assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: radio immuno assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: type II interferon production
        intersection of: Restriction
subclass of: radio immuno assay
subclass of: assay measuring epitope specific interferon-gamma production by T cells
editor preferred term: radio immuno assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120
definition: A radio immuno assay that detects interferon-gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IFNg release|radio immuno assay (RIA)

DNA methylation profiling by high throughput sequencing design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: epigenetic modification identification objective
editor preferred term: DNA methylation profiling by high throughput sequencing design
has curation status: IAO_0000120
definition: A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: GROUP: ArrayExpress production team

assay measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
subclass of: assay measuring epitope specific cytotoxic T cell degranulation
editor preferred term: assay measuring epitope specific granzyme B release by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: granzyme B release|biological activity

intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-X-C motif) ligand 9 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CXCL9/MIG release|ICS

ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: macrophage inflammatory protein-1 gamma production
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
editor preferred term: ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL9/MIP-1g release|ELISA

epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: chemokine (C-X-C motif) ligand 9 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: chemokine (C-X-C motif) ligand 9 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
has curation status: IAO_0000122
definition: A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

all pairs design
type: Class
subclass of: OBI_0500000
editor preferred term: all pairs design
has curation status: IAO_0000120
definition: A study design in which all specimens are compared to every other specimen.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_565 all_pairs

proteomic profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
editor preferred term: proteomic profiling by array design
has curation status: IAO_0000120
definition: A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology.
term editor: Person: Chris Stoeckert, Jie Zheng, Dan Berrios
definition source: Group: ArrayExpress production team
term tracker item: https://github.com/obi-ontology/obi/issues/854

q-value
type: Class
subclass of: quantitative confidence value
editor preferred term: q-value
example of usage: PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
has curation status: IAO_0000122
definition: A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
term editor: PERS:Philippe Rocca-Serra
alternative label: FDR adjusted p-value
definition source: Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html

genotyping design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: sequence feature identification objective
editor preferred term: genotyping design
has curation status: IAO_0000120
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_560 genotyping_design

assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-2 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-2 release|biological activity

epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-15 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-15 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific interleukin-15 production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: macrophage inflammatory protein-1 gamma production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: macrophage inflammatory protein-1 gamma production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific macrophage inflammatory protein-1 gamma production by T cells
has curation status: IAO_0000122
definition: A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

individual genetic characteristics comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: genetic characteristics information
editor preferred term: individual genetic characteristics comparison design
has curation status: IAO_0000120
definition: A study design where genotype, haplotype, or other individual genetic characteristics are compared.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_527 individual_genetic_characteristics_design

assay measuring epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-1 beta production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-1 beta production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-1b release|biological activity

assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-4 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-4 release|biological activity

assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-6 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-6 release|biological activity

cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells
type: Class
equivalent class: Class
  intersection of: reporter cell line analyte detection bioassay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: tumor necrosis factor production
        intersection of: Restriction
subclass of: assay measuring epitope specific tumor necrosis factor alpha production by T cells
subclass of: OBI_0003488
editor preferred term: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells
has curation status: IAO_0000120
definition: A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: TNFa release|bioassay

intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: lymphotoxin A production
        intersection of: Restriction
subclass of: assay measuring epitope specific lymphotoxin A production by T cells
subclass of: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects lymphotoxin A production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: lymphotoxin A/TNFb release|ICS

pathogenicity design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
editor preferred term: pathogenicity design
has curation status: IAO_0000120
definition: A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_807 pathogenicity_design

ELISPOT assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0600031
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-5 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-5 production by T cells
subclass of: OBI_0600031
editor preferred term: ELISPOT assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunospot assay that detects interleukin-5 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-5 release|ELISPOT

assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: macrophage inflammatory protein-1 gamma production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL9/MIP-1g release|biological activity

cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-8 production
        intersection of: Restriction
subclass of: assay measuring epitope specific interleukin-8 production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-8 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-8 release|cytometric bead array

assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: chemokine (C-X-C motif) ligand 9 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CXCL9/MIG release|biological activity

genetic modification design
type: Class
subclass of: intervention design
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study intervention
        intersection of: OBI_0600043
editor preferred term: genetic modification design
has curation status: IAO_0000120
definition: A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_447 genetic_modification_design

ELISA measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunosorbent assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003319
        intersection of: Restriction
subclass of: enzyme-linked immunosorbent assay
subclass of: assay measuring epitope specific granzyme B release by T cells
editor preferred term: ELISA measuring epitope specific granzyme B release by T cells
has curation status: IAO_0000120
definition: An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: granzyme B release|ELISA

epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: IP-10 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: IP-10 production
subclass of: epitope specific cytokine production by T cells
editor preferred term: epitope specific IP-10 production by T cells
has curation status: IAO_0000122
definition: A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

transcription profiling by array assay
type: Class
subclass of: transcription profiling assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: characteristic of
        some values from: OBI_0400148
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_0400148
editor preferred term: transcription profiling by array assay
has curation status: IAO_0000120
definition: A transcription profiling assay that uses array technology.
term editor: James Malone
alternative label: RNA profiling by array assay
definition source: EFO:0002768
term tracker item: https://sourceforge.net/p/obi/obi-terms/757/

strain comparison design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: selectively maintained organism
editor preferred term: strain comparison design
has curation status: IAO_0000120
definition: A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_462 strain_or_line_design

assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: monocyte chemotactic protein-1 production
        intersection of: Restriction
subclass of: OBI_1110129
editor preferred term: assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: CCL2/MCP-1 release|biological activity

intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-12 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-12 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-12 production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: IL-12 release|ICS

in vivo assay measuring T cell epitope specific disease exacerbation
type: Class
equivalent class: Class
  intersection of: epitope disease exacerbation experiment
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
subclass of: epitope disease exacerbation experiment
subclass of: assay measuring T cell epitope specific in vivo activity
editor preferred term: in vivo assay measuring T cell epitope specific disease exacerbation
has curation status: IAO_0000120
definition: An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
term editor: IEDB
definition source: IEDB
IEDB alternative term: disease exacerbation|in vivo assay

cell specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: has part
    some values from: cell
subclass of: specimen from organism
editor preferred term: cell specimen
has curation status: IAO_0000123
definition: A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
editor note: 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
term editor: PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
definition source: MO_612 cell

monospecific T cell recognition assay measuring MHC ligand processing and presentation
type: Class
subclass of: OBI_1110125
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_1110037
editor preferred term: monospecific T cell recognition assay measuring MHC ligand processing and presentation
has curation status: IAO_0000120
definition: A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: ligand presentation|T cell recognition

epitope specific interleukin-17F production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-17F production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-17F production
subclass of: OBI_1110193
editor preferred term: epitope specific interleukin-17F production by T cells
has curation status: IAO_0000122
definition: A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB (QTT)
curator note: Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl

T cell epitope specific immune intervention
type: Class
subclass of: epitope specific immune intervention
editor preferred term: T cell epitope specific immune intervention
example of usage: Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
has curation status: IAO_0000120
definition: An epitope specific immune intervention in which the induced response targets a T cell epitope
term editor: PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB

specimen with known storage state
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Class
    union of: fresh specimen
    union of: Class
      intersection of: OBI_0100051
      intersection of: Restriction
        on property: is specified output of
        some values from: OBI_0302893
subclass of: OBI_0100051
editor preferred term: specimen with known storage state
has curation status: IAO_0000123
definition: A specimen for which it is known whether it has been subjected to storage of a specified type.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_95 BiosourceType

in vivo assay measuring T cell epitope specific protection after tumor burden challenge
type: Class
equivalent class: Class
  intersection of: OBI_0003458
  intersection of: Restriction
    on property: has part
    some values from: OBI_0003414
  intersection of: Restriction
    on property: has part
    some values from: OBI_0003455
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
subclass of: OBI_0003458
subclass of: OBI_0003461
editor preferred term: in vivo assay measuring T cell epitope specific protection after tumor burden challenge
has curation status: IAO_0000120
definition: An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden.
term editor: IEDB
definition source: IEDB
IEDB alternative term: tumor burden after challenge|in vivo assay

lowess group transformation
type: Class
subclass of: lowess transformation
editor preferred term: lowess group transformation
has curation status: IAO_0000120
definition: 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.
term editor: Person: Elisabetta Manduchi
definition source: MO_861 lowess_group_normalization

in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
type: Class
equivalent class: Class
  intersection of: epitope protection from infectious challenge experiment based on pathogen burden
  intersection of: Restriction
    on property: has part
    some values from: pathogen challenge
  intersection of: Restriction
    on property: has part
    some values from: OBI_0003414
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
subclass of: epitope protection from infectious challenge experiment based on pathogen burden
subclass of: OBI_0003460
editor preferred term: in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
has curation status: IAO_0000120
definition: An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden.
term editor: IEDB
definition source: IEDB
IEDB alternative term: pathogen burden after challenge|in vivo assay

phage display binding assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has part
    some values from: phage display library panning
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: OBI_0003368
      intersection of: OBI_0600047
  intersection of: Restriction
    on property: has specified input
    some values from: OBI_1000029
subclass of: binding assay
editor preferred term: phage display binding assay
example of usage: Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated.
has curation status: IAO_0000120
definition: A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner.
term editor: IEDB
definition source: IEDB

lowess transformation
type: Class
subclass of: OBI_0200169
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200167
editor preferred term: lowess transformation
has curation status: IAO_0000120
definition: 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.
term editor: Person: Elisabetta Manduchi
definition source: MO_720 lowess_normalization

mass spectrometry assay measuring MHC ligand processing and presentation
type: Class
equivalent class: Class
  intersection of: OBI_1110125
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: mass spectrometry assay
      intersection of: OBI_0003368
subclass of: OBI_1110125
editor preferred term: mass spectrometry assay measuring MHC ligand processing and presentation
has curation status: IAO_0000120
definition: A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands
term editor: IEDB
definition source: IEDB
IEDB alternative term: ligand presentation|mass spectrometry

specimen from organism
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: OBI_0100051
editor preferred term: specimen from organism
has curation status: IAO_0000122
definition: 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).
term editor: PERSON: Chris Stoeckert, Jie Zheng
alternative label: tissue specimen
definition source: MO_954 organism_part

phage display library panning
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: OBI_1000029
editor preferred term: phage display library panning
example of usage: 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.
has curation status: IAO_0000120
definition: 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.
term editor: Jason Greenbaum, Randi Vita, Bjoern Peters
definition source: IEDB, http://en.wikipedia.org/wiki/Phage_display

lowess global transformation
type: Class
subclass of: lowess transformation
editor preferred term: lowess global transformation
has curation status: IAO_0000120
definition: 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.
term editor: Person: Elisabetta Manduchi
definition source: MO_692 lowess_global_normalization

intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: transforming growth factor beta production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific transforming growth factor-beta production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects transforming growth factor-beta production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: TGFb release|ICS

cell collecting
type: Class
subclass of: OBI_0600014
subclass of: Restriction
  on property: has specified input
  some values from: OBI_0100060
subclass of: Restriction
  on property: has specified output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has grain
      some values from: cell
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
editor preferred term: cell collecting
has curation status: IAO_0000120
definition: A planned process that collects cells from culture.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_982 harvest

assay measuring T cell epitope specific in vivo activity
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
subclass of: OBI_0002055
editor preferred term: assay measuring T cell epitope specific in vivo activity
has curation status: IAO_0000120
definition: A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
term editor: IEDB
definition source: IEDB
IEDB alternative term: in vivo activity|biological activity

purified MHC molecule preparation
type: Class
subclass of: OBI_0001633
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: MHC protein complex
  intersection of: Restriction
    on property: is specified output of
    some values from: purification
editor preferred term: purified MHC molecule preparation
example of usage: HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody.
has curation status: IAO_0000120
definition: A mixture containing MHC molecules that was purified to remove non-MHC molecular entities.
editor note: BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general.
term editor: Bjoern Peters

disposition to be bound by an MHC protein complex
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized in
  all values from: MHC protein complex binding to ligand
editor preferred term: disposition to be bound by an MHC protein complex
has curation status: IAO_0000120
definition: 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.
term editor: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
alternative label: MHC ligand disposition
definition source: IEDB

B cell epitope specific immune intervention
type: Class
subclass of: epitope specific immune intervention
editor preferred term: B cell epitope specific immune intervention
example of usage: Injecting a mouse with recombinant antibody targeting an anthrax epitope
has curation status: IAO_0000120
definition: An epitope specific immune intervention in which the induced response targets a B cell epitope
term editor: PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB

epitope tolerance induction experiment
type: Class
subclass of: efficacy of epitope intervention experiment
editor preferred term: epitope tolerance induction experiment
has curation status: IAO_0000120
definition: An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
term editor: IEDB
alternative label: tolerance induction
definition source: IEDB

mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC
type: Class
subclass of: mass spectrometry assay measuring MHC ligand processing and presentation
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: mass spectrometry assay
    intersection of: OBI_0003368
editor preferred term: mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC
has curation status: IAO_0000120
definition: A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC.
term editor: IEDB
definition source: IEDB
IEDB alternative term: ligand presentation|cellular MHC/mass spectrometry

cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: granulocyte macrophage colony-stimulating factor production
        intersection of: Restriction
subclass of: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
subclass of: OBI_0003115
editor preferred term: cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: GM-CSF release|cytometric bead array

binding assay using radioactivity detection
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: radioactivity detection
      intersection of: OBI_0003368
subclass of: binding assay
editor preferred term: binding assay using radioactivity detection
has curation status: IAO_0000120
definition: A binding assay that uses radioactivity detection as an indicator of binding.
term editor: Bjoern Peters
term editor: Randi Vita
definition source: IEDB

in vivo assay measuring T cell epitope specific protection based on survival
type: Class
equivalent class: Class
  intersection of: epitope protection experiment based on survival
  intersection of: Restriction
    on property: has part
    some values from: OBI_0003414
  intersection of: Restriction
    on property: has part
    some values from: Class
      complement of: Class
        union of: pathogen challenge
        union of: OBI_0003455
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
subclass of: epitope protection experiment based on survival
subclass of: OBI_0003462
editor preferred term: in vivo assay measuring T cell epitope specific protection based on survival
has curation status: IAO_0000120
definition: An in vivo assay measuring T cell epitope specific protection from other challenge using survival.
term editor: IEDB
definition source: IEDB
IEDB alternative term: survival from challenge|in vivo assay

cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
type: Class
subclass of: OBI_0001550
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_1110037
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: OBI_0001955
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: cell
    intersection of: Restriction
      on property: has part
      some values from: MHC protein complex
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: MHC protein complex binding to ligand
editor preferred term: cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
has curation status: IAO_0000120
definition: A cell bound MHC binding assay that uses a T cell epitope recognition assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: qualitative binding|cellular MHC/T cell inhibition

linear amplification
type: Class
subclass of: OBI_0600058
editor preferred term: linear amplification
example of usage: An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
has curation status: IAO_0000120
definition: An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_997 linear_amplification

in vivo assay measuring epitope specific T cell helper activity
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: helper T cell enhancement of adaptive immune response
        intersection of: Restriction
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
subclass of: assay measuring T cell epitope specific in vivo activity
editor preferred term: in vivo assay measuring epitope specific T cell helper activity
has curation status: IAO_0000120
definition: A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function.
term editor: IEDB
definition source: IEDB
IEDB alternative term: helper response|in vivo assay

intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: flow cytometry assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-22 production
        intersection of: Restriction
subclass of: flow cytometry assay
subclass of: assay measuring epitope specific interleukin-22 production by T cells
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
has curation status: IAO_0000120
definition: A flow cytometry assay that detects interleukin-22 production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-22 release|ICS

assay measuring epitope specific perforin release by T cells
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: OBI_0003317
        intersection of: Restriction
subclass of: assay measuring epitope specific cytotoxic T cell degranulation
editor preferred term: assay measuring epitope specific perforin release by T cells
has curation status: IAO_0000120
definition: A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: perforin release|biological activity

atmosphere
type: Class
subclass of: growth environment
editor preferred term: atmosphere
has curation status: IAO_0000120
definition: A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_219 atmosphere

binding assay using fluorescence detection
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: fluorescence detection assay
      intersection of: OBI_0003368
subclass of: binding assay
editor preferred term: binding assay using fluorescence detection
has curation status: IAO_0000120
definition: A binding assay that uses fluorescence detection as an indicator of binding.
term editor: Bjoern Peters
term editor: Randi Vita
definition source: IEDB

coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand
type: Class
subclass of: OBI_1110125
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0003368
    intersection of: OBI_1110037
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: positive reference substance role
editor preferred term: coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand
has curation status: IAO_0000120
definition: A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: ligand presentation|coelution

fluorescence detection assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has characteristic
        some values from: PATO_0000018
subclass of: assay
editor preferred term: fluorescence detection assay
example of usage: Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
has curation status: IAO_0000120
definition: An assay in which a material's fluorescence is determined.
term editor: IEDB
definition source: IEDB

epitope specific perforin production by T cells
type: Class
subclass of: perforin production
subclass of: Class
  intersection of: perforin production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
editor preferred term: epitope specific perforin production by T cells
has curation status: IAO_0000120
definition: The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
editor note: 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
term editor: PERSON: Bjoern Peters, Randi Vita

MHC protein complex binding to ligand
type: Class
subclass of: OBI_0001588
subclass of: Class
  intersection of: OBI_0001588
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: disposition
      intersection of: Restriction
        on property: characteristic of
        some values from: Class
editor preferred term: MHC protein complex binding to ligand
example of usage: The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
has curation status: IAO_0000120
definition: The process in which a ligand binds to an MHC molecule to form a stable complex.
editor note: 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.
term editor: PERSON: Bjoern Peters; Randi Vita
definition source: IEDB

dissection
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred term: dissection
has curation status: IAO_0000120
definition: A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: EFO_0003856 dissection
definition source: MO_374 dissect

purification
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: purification objective
subclass of: OBI_0600014
editor preferred term: purification
has curation status: IAO_0000120
definition: 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
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_406 purify

specimen with pre- or post-mortem status
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen from organism
editor preferred term: specimen with pre- or post-mortem status
has curation status: IAO_0000120
definition: A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
editor note: organizational term, used in description of specimen that is created from known pre- or post-mortem status
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_84 OrganismStatus

in vivo assay measuring T cell epitope specific treatment of disease
type: Class
equivalent class: Class
  intersection of: epitope treatment experiment
  intersection of: Restriction
    on property: has part
    some values from: OBI_0003414
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: has assay target context
        some values from: Class
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: process is result of
        some values from: OBI_1110057
subclass of: epitope treatment experiment
subclass of: assay measuring T cell epitope specific in vivo activity
editor preferred term: in vivo assay measuring T cell epitope specific treatment of disease
has curation status: IAO_0000120
definition: An efficacy of T cell epitope intervention experiment that detects a decrease in disease.
term editor: IEDB
definition source: IEDB
IEDB alternative term: decreased disease|in vivo assay

sampling time measurement datum
type: Class
subclass of: time measurement datum
editor preferred term: sampling time measurement datum
has curation status: IAO_0000120
definition: A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
term editor: Person: Chris Stoeckert
alternative label: time point
definition source: MO_738 timepoint

Edman degradation assay measuring MHC ligand processing and presentation
type: Class
equivalent class: Class
  intersection of: OBI_1110125
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: Edman degradation
      intersection of: OBI_0003368
subclass of: OBI_1110125
editor preferred term: Edman degradation assay measuring MHC ligand processing and presentation
has curation status: IAO_0000120
definition: A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: ligand presentation|Edman degradation

mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC
type: Class
subclass of: mass spectrometry assay measuring MHC ligand processing and presentation
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: mass spectrometry assay
    intersection of: OBI_0003368
editor preferred term: mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC
has curation status: IAO_0000120
definition: A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC.
term editor: IEDB
definition source: IEDB
IEDB alternative term: ligand presentation|secreted MHC/mass spectrometry

disposition to be a product of antigen processing and presentation
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized in
  all values from: antigen processing and presentation
editor preferred term: disposition to be a product of antigen processing and presentation
example of usage: 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.
has curation status: IAO_0000120
definition: 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.
term editor: IEDB
definition source: IEDB

cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0003115
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: Class
        intersection of: interleukin-17A production
        intersection of: Restriction
subclass of: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
subclass of: OBI_0001773
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
has curation status: IAO_0000120
definition: A cytometric bead array assay that detects interleukin-17A production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-17A release|cytometric bead array

radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex
type: Class
subclass of: binding assay using radioactivity detection
subclass of: OBI_0001555
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: OBI_0001955
subclass of: Restriction
  on property: has specified input
  some values from: Class
    intersection of: purified MHC molecule preparation
    intersection of: Restriction
      on property: has part
      some values from: MHC protein complex
subclass of: Restriction
  on property: has specified output
  some values from: OBI_0003141
subclass of: Restriction
  on property: has specified output
  some values from: Restriction
    on property: is about
    some values from: MHC protein complex binding to ligand
editor preferred term: radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex
has curation status: IAO_0000120
definition: A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: qualitative binding|purified MHC/competitive/radioactivity

minimal inhibitory concentration
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
subclass of: Restriction
  on property: is about
  some values from: dose response curve
editor preferred term: minimal inhibitory concentration
has curation status: IAO_0000120
definition: 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.
editor note: Created following request by Albert Goldfain
term editor: PERSON:Bjoern Peters
definition source: Bjoern Peters, coordinated with Albert Goldfain

material maintenance service
type: Class
equivalent class: Class
  intersection of: OBI_0001528
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: material maintenance
subclass of: OBI_0001528
editor preferred term: material maintenance service
example of usage: model organism colony maintanance
has curation status: IAO_0000125
definition: 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.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
comment: Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.

radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: OBI_1000036
      intersection of: Restriction
        on property: has part
        some values from: MHC protein complex
  intersection of: Restriction
    on property: has specified output
    some values from: OBI_0003143
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: is about
      some values from: MHC protein complex binding to ligand
  intersection of: Restriction
    on property: has specified output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: binding assay using radioactivity detection
subclass of: OBI_0001991
editor preferred term: radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex
has curation status: IAO_0000120
definition: A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM

radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: binding assay using radioactivity detection
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has role
        some values from: OBI_0001955
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: cell
      intersection of: Restriction
        on property: has part
        some values from: MHC protein complex
subclass of: binding assay using radioactivity detection
subclass of: OBI_0001992
editor preferred term: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex
has curation status: IAO_0000120
definition: A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
IEDB alternative term: half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM