Ontology for Biomedical Investigation
type: Ontology
version info: 2017-02-22
version IRI: OBI Release 2017-02-22
creator: Pierre Grenon
creator: Bjoern Peters
creator: Matthew Pocock
creator: Liju Fan
creator: Christian Bolling
creator: Chris Taylor
creator: Chris Stoeckert
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.
creator: Tina Hernandez-Boussard
creator: Jessica Turner
creator: Allyson Lister
creator: Yongqun He
creator: Jie Zheng
creator: Tanya Gray
date: 2009-07-31
license: http://creativecommons.org/licenses/by/3.0/
creator: Bill Bug
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Lawrence Hunter
description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
creator: Chris Mungall
creator: Daniel Schober
creator: Helen C. Causton
creator: James Malone
creator: Kevin Clancy
creator: Susanna-Assunta Sansone
creator: Norman Morrison
creator: Daniel Rubin
creator: Cristian Cocos
creator: Stefan Wiemann
subject: An ontology for the annotation of biomedical and functional genomics experiments.
creator: Melanie Courtot
creator: Helen Parkinson
creator: Luisa Montecchi
creator: Jennifer Fostel
creator: Jeffrey Grethe
creator: Eric Deutsch
creator: Philip Lord
creator: Gilberto Fragoso
creator: Philippe Rocca-Serra
creator: Elisabetta Manduchi
Format: OWL-DL
creator: Mervi Heiskanen
creator: Richard Bruskiewich
creator: Robert Stevens
creator: Dirk Derom
creator: Larisa Soldatova
creator: James A. Overton
creator: Dawn Field
creator: Trish Whetzel
creator: Alan Ruttenberg
creator: Frank Gibson
creator: Matthew Brush
creator: Richard Scheuermann
creator: John Westbrook
creator: Barry Smith
creator: Carlo Torniai
default language: en
creator: Jay Greenbaum
creator: Ryan R. Brinkman
creator: Monnie McGee
creator: Holger Stenzhorn
creator: Melissa Haendel
creator: Joe White
type: NamedIndividual

OBI Release 2017-02-22
type: Thing
type: Version
file-release: Ontology for Biomedical Investigation
revision: SVN Revision: Unversioned directory
type: NamedIndividual

BFO OWL specification label
type: AnnotationProperty
editor preferred term: BFO OWL specification label
curator note: Really of interest to developers only
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.
sub property of: label

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

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

example of usage
type: AnnotationProperty
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: example of usage
has curation status: IAO_0000122

in branch
type: AnnotationProperty
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
editor preferred term: in branch

has curation status
type: AnnotationProperty
definition source: OBI_0000281
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
editor preferred term: has curation status

definition
type: AnnotationProperty
label: textual definition
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.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
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 preferred term: definition
has curation status: IAO_0000122

editor note
type: AnnotationProperty
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.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: IAO_0000122

term editor
type: AnnotationProperty
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
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
term editor: PERSON:Daniel Schober
editor preferred term: term editor
has curation status: IAO_0000122

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: alternative term
has curation status: IAO_0000125

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: definition source
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
has curation status: IAO_0000122

has obsolescence reason
type: AnnotationProperty
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
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.
editor preferred term: has obsolescence reason

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

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

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

expand expression to
type: AnnotationProperty
term editor: Chris Mungall
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
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)"
editor preferred term: expand expression to

expand assertion to
type: AnnotationProperty
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall
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)"
editor preferred term: expand assertion to

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

antisymmetric property
type: AnnotationProperty
term editor: Alan Ruttenberg
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

OBO foundry unique label
type: AnnotationProperty
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 .
definition: An alternative name for a class or property which is unique across the OBO Foundry.
definition source: GROUP:OBO Foundry <http://obofoundry.org/>
editor preferred term: OBO foundry unique label
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
has curation status: IAO_0000125

has ID digit count
type: AnnotationProperty
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)
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"
term editor: Person:Alan Ruttenberg
editor preferred term: has ID digit count

has ID range allocated to
type: AnnotationProperty
term editor: Person:Alan Ruttenberg
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
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
editor preferred term: has ID range allocated to

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
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
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"
editor preferred term: has ID prefix

elucidation
type: AnnotationProperty
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
editor preferred term: elucidation
term editor: person:Alan Ruttenberg

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

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

is allocated id range
type: AnnotationProperty
definition: Add as annotation triples in the granting ontology
term editor: PERSON:Alan Ruttenberg
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"
editor preferred term: is allocated id range

retired from use as of
type: AnnotationProperty
term editor: Alan Ruttenberg
editor note: In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
definition: relates a class of CRID to the date after which further instances should not be made, according to the central authority
editor preferred term: retired from use as of

has axiom label
type: AnnotationProperty
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
definition source: Person:Alan Ruttenberg
term editor: Person:Alan Ruttenberg
editor preferred term: has axiom label

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

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

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

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

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

temporal interpretation
type: AnnotationProperty
editor preferred term: temporal interpretation

Contributor
type: AnnotationProperty
comment: An entity responsible for making contributions to the content of the resource.
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.

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
comment: An entity primarily responsible for making the content of the resource.
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.

Date
type: AnnotationProperty
comment: A date associated with an event in the life cycle of the resource.
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.

Description
type: AnnotationProperty
comment: An account of the content of the resource.
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.

Format
type: AnnotationProperty
comment: The physical or digital manifestation of the resource.
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).

Resource Identifier
type: AnnotationProperty
comment: An unambiguous reference to the resource within a given context.
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).

Language
type: AnnotationProperty
comment: A language of the intellectual content of the resource.
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.

Publisher
type: AnnotationProperty
comment: An entity responsible for making the resource available
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.

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
comment: A reference to a resource from which the present resource is derived.
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.

Subject and Keywords
type: AnnotationProperty
comment: The topic of the content of the resource.
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.

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
comment: The nature or genre of the content of the resource.
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.

shorthand
type: AnnotationProperty
editor preferred term: shorthand

label
type: AnnotationProperty

part of
type: ObjectProperty
type: TransitiveProperty
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
definition: a core relation that holds between a part and its whole
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)
editor preferred term: part of
alternative term: part_of
example of usage: this day is part of this year (occurrent parthood)
inverse of: has part
temporal interpretation: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
definition: a core relation that holds between a whole and its part
editor preferred term: has part
alternative 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)
temporal interpretation: RO_0001901

realized in
type: ObjectProperty
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
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])
alternative term: is realized by
editor preferred term: realized in
alternative 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
range: process
domain: realizable entity

realizes
type: ObjectProperty
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
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])
domain: process
range: realizable entity
inverse of: realized in

preceded by
type: ObjectProperty
type: TransitiveProperty
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.
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
alternative term: is preceded by
editor preferred term: preceded by
alternative term: preceded_by
range: occurrent
domain: occurrent
inverse of: precedes

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

occurs in
type: ObjectProperty
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
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
editor preferred term: occurs in
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
domain: occurrent
range: independent continuant
inverse of: contains process
property chain axiom: part of

contains process
type: ObjectProperty
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
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
editor preferred term: contains process

has measurement unit label
type: ObjectProperty
type: FunctionalProperty
editor preferred term: has measurement unit label
sub property of: has part
range: measurement unit label

obsolete_specifically denotes
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
term editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
definition: c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
editor preferred term: obsolete_specifically denotes
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000125
sub property of: ObsoleteProperty

is about
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
editor preferred term: is about
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
term editor: person:Alan Ruttenberg
domain: information content entity
has curation status: IAO_0000125

mentions
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
term editor: PERSON: Jonathan Rees
term editor: Person: Alan Ruttenberg
editor preferred term: mentions
has curation status: IAO_0000125
sub property of: is about

denotes
type: ObjectProperty
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
editor preferred term: denotes
definition: denotes is 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
term editor: person:Alan Ruttenberg
sub property of: is about

obsolete_materially denotes
type: ObjectProperty
editor preferred term: obsolete_materially denotes
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
deprecated: true
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

is quality measurement of
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
term editor: Alan Ruttenberg
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
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
range: quality
domain: measurement datum
sub property of: is about

obsolete_describes
type: ObjectProperty
editor preferred term: obsolete_describes
deprecated: true
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

obsolete_represents
type: ObjectProperty
editor preferred term: obsolete_represents
deprecated: true
has obsolescence reason: IAO_0000103
sub property of: ObsoleteProperty

has coordinate unit label
type: ObjectProperty
type: FunctionalProperty
editor preferred term: has coordinate unit label
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
sub property of: has part
domain: cartesian spatial coordinate datum
range: UO_0000001

is duration of
type: ObjectProperty
term editor: Person:Alan Ruttenberg
editor preferred term: is duration of
definition: relates a process to a time-measurement-datum that represents the duration of the process
range: process
has curation status: IAO_0000120
sub property of: is about
domain: time measurement datum

is quality measured as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg
definition: inverse of the relation of is quality measurement of
editor preferred term: is quality measured as
has curation status: IAO_0000120
inverse of: is quality measurement of

is quality specification of
type: ObjectProperty
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
definition: a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
editor preferred term: is quality specification of
has curation status: IAO_0000120
sub property of: is about

quality is specified as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
definition: inverse of the relation of is quality specification of
editor preferred term: quality is specified as
has curation status: IAO_0000120
inverse of: is quality specification of

has time stamp
type: ObjectProperty
type: FunctionalProperty
term editor: Alan Ruttenberg
editor preferred term: has time stamp
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
sub property of: has part
has curation status: IAO_0000123
range: time measurement datum
domain: time stamped measurement datum

has measurement datum
type: ObjectProperty
term editor: Alan Ruttenberg
editor preferred term: has measurement datum
definition: relates a time stamped measurement datum to the measurement datum that was measured
sub property of: has part
has curation status: IAO_0000123
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum

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

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

has_specified_input
type: ObjectProperty
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: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
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: PERSON: Alan Ruttenberg
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
domain: planned process
inverse of: is_specified_input_of
sub property of: has participant
imported from: Ontology for Biomedical Investigation

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

is_specified_input_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
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
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
range: planned process
sub property of: participates in

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

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

has_specified_output
type: ObjectProperty
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
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: PERSON: Alan Ruttenberg
editor preferred term: has_specified_output
has curation status: IAO_0000122
domain: planned process
inverse of: is_specified_output_of
sub property of: has participant
imported from: Ontology for Biomedical Investigation

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

obsoleted_has_specified_output_information
type: ObjectProperty
term editor: PERSON: Frank Gibson
deprecated: true
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
editor preferred term: obsoleted_has_specified_output_information
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123
sub property of: ObsoleteProperty

is_manufactured_by
type: ObjectProperty
term editor: Alan Ruttenberg
term editor: Liju Fan
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.
alternative term: has_make
alternative term: has_manufacturer
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)
editor preferred term: is_manufactured_by
domain: material entity
has curation status: IAO_0000123
range: Class
  union of: Homo sapiens
  union of: organization

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

obsoleted_is_reagent_in
type: ObjectProperty
deprecated: true
term editor: Alan Ruttenberg
definition: Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
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 obsolescence reason: IAO_0000103
has curation status: IAO_0000123
sub property of: ObsoleteProperty

obsolete_realizes
type: ObjectProperty
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungal
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]
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.
alternative term: executes
alternative term: has_function_part
alternative term: involves_execution_of
alternative term: is_realization_of
editor note: replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'
deprecated: true
editor preferred term: obsolete_realizes
has curation status: IAO_0000122
has obsolescence reason: IAO_0000228
sub property of: ObsoleteProperty

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

obsoleted_is_device_for
type: ObjectProperty
deprecated: true
term editor: Alan Ruttenberg
definition: Relationship between a device and a protocol application in which it participates
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 obsolescence reason: IAO_0000103
has curation status: IAO_0000123
sub property of: ObsoleteProperty

is_specified_output_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
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
editor preferred term: is_specified_output_of
has curation status: IAO_0000122
range: planned process
sub property of: participates in
imported from: Ontology for Biomedical Investigation

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

is_proxy_for
type: ObjectProperty
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)
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.
term editor: Alan Ruttenberg
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
domain: continuant
range: continuant
has curation status: IAO_0000123

obsoleted_has_specified_input_information
type: ObjectProperty
term editor: PERSON: Frank Gibson
alternative term: consumes data
deprecated: true
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:Alan Ruttenberg
editor preferred term: obsoleted_has_specified_input_information
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123
sub property of: ObsoleteProperty

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

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

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

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

has grain
type: ObjectProperty
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
editor preferred term: has grain
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
sub property of: has part
has curation status: IAO_0000120

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

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

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

has_supplier
type: ObjectProperty
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
editor preferred term: has_supplier
domain: material entity
has curation status: IAO_0000120
range: Class
  union of: Homo sapiens
  union of: organization

objective_achieved_by
type: ObjectProperty
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
editor preferred term: objective_achieved_by
definition source: OBI
term editor: OBI
domain: objective specification
has curation status: IAO_0000122
range: planned process

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

has category label
type: ObjectProperty
editor preferred term: has category label
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.
sub property of: has part
has curation status: IAO_0000123
domain: categorical measurement datum
range: categorical label

has disposition to bind
type: ObjectProperty
type: SymmetricProperty
definition: A relationship between two material entitites that each have disposition to form a complex with the other.
definition source: IEDB
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
editor preferred term: has disposition to bind
domain: material entity
range: material entity
has curation status: IAO_0000123

has organization member
type: ObjectProperty
term editor: Person: Jie Zheng
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
editor preferred term: has organization member
has curation status: IAO_0000123
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization

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

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

has performer
type: ObjectProperty
editor preferred term: has performer
term editor: 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 curation status: IAO_0000428
domain: planned process
sub property of: has participant
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

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

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

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

inheres in
type: ObjectProperty
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor preferred term: inheres in
alternative term: inheres_in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
temporal interpretation: RO_0001901

bearer of
type: ObjectProperty
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.
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor preferred term: bearer of
alternative term: bearer_of
alternative term: is bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
range: specifically dependent continuant
inverse of: inheres in
temporal interpretation: RO_0001901

participates in
type: ObjectProperty
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
editor preferred term: participates in
alternative 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
domain: continuant
range: occurrent

has participant
type: ObjectProperty
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.
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor preferred term: has participant
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
alternative 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)
range: continuant
domain: occurrent
inverse of: participates in

is concretized as
type: ObjectProperty
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).
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.
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).
editor preferred term: is concretized as
range: specifically dependent continuant
domain: generically dependent continuant

concretizes
type: ObjectProperty
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).
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.
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).
editor preferred term: concretizes
domain: specifically dependent continuant
range: generically dependent continuant
inverse of: is concretized as

function of
type: ObjectProperty
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.
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 preferred term: function of
alternative term: function_of
alternative term: is function of
example of usage: this catalysis function is a function of this enzyme
domain: function
sub property of: inheres in
inverse of: has function

quality of
type: ObjectProperty
editor note: A quality inheres in its bearer at all times for which the quality exists.
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
alternative term: is quality of
editor preferred term: quality of
alternative term: quality_of
example of usage: this red color is a quality of this apple
sub property of: inheres in
inverse of: has quality

role of
type: ObjectProperty
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.
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
alternative term: is role of
editor preferred term: role of
alternative term: role_of
example of usage: this investigator role is a role of this person
sub property of: inheres in

has function
type: ObjectProperty
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.
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 preferred term: has function
alternative term: has_function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
range: function
sub property of: bearer of

has quality
type: ObjectProperty
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.
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 preferred term: has quality
alternative term: has_quality
example of usage: this apple has quality this red color
range: quality
sub property of: bearer of

has role
type: ObjectProperty
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.
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 preferred term: has role
alternative term: has_role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
domain: independent continuant
range: role
sub property of: bearer of
inverse of: role of

derives from
type: ObjectProperty
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
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 preferred term: derives from
alternative 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)
domain: independent continuant
range: independent continuant
has curation status: IAO_0000125
imported from: ro.owl
sub property of: topObjectProperty

derives into
type: ObjectProperty
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'.
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 preferred term: derives into
alternative term: derives_into
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
inverse of: derives from

location of
type: ObjectProperty
type: TransitiveProperty
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor preferred term: location of
alternative term: location_of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
temporal interpretation: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor preferred term: located in
alternative term: located_in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
inverse of: location of
temporal interpretation: RO_0001901

2D boundary of
type: ObjectProperty
editor preferred term: 2D boundary of
alternative term: 2D_boundary_of
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.
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of
example of usage: the surface of my skin is a 2D boundary of my body
temporal interpretation: RO_0001901

has 2D boundary
type: ObjectProperty
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.
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor preferred term: has 2D boundary
alternative term: has boundary
alternative term: has_2D_boundary
example of usage: my body has 2D boundary the surface of my skin
domain: material entity
range: immaterial entity
temporal interpretation: RO_0001901
inverse of: 2D boundary of

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

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

surrounded by
type: ObjectProperty
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
editor preferred term: surrounded by
sub property of: adjacent to
imported from: ro.owl

adjacent to
type: ObjectProperty
editor preferred term: adjacent to

temporal relation
type: ObjectProperty
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.
editor preferred term: temporal relation
range: occurrent
has curation status: IAO_0000125

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

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

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

has measurement value
type: DatatypeProperty
type: FunctionalProperty
editor preferred term: has measurement value
domain: scalar measurement datum
range: float

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
editor preferred term: has x coordinate value
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
editor preferred term: has z coordinate value
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
editor preferred term: has y coordinate value
domain: cartesian spatial coordinate datum
range: float

has_feature_value
type: DatatypeProperty
term editor: James Malone
editor preferred term: has_feature_value
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.
has curation status: IAO_0000123
domain: OBI_0200140

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

entity
type: Class
subclass of: Thing
disjoint with: ObsoleteClass
BFO OWL specification label: entity
BFO CLIF specification label: Entity
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
editor preferred term: entity
example of usage: the Second World War
example of usage: your body mass index

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

Axiom
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
comment: per discussion with Barry Smith
annotated source: entity
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004

continuant
type: Class
subclass of: entity
disjoint with: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
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 (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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])
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
editor preferred term: continuant
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])

Axiom
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
annotated source: continuant
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

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

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

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

Axiom
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])
annotated source: continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

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

Axiom
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])
annotated source: continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
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])
annotated source: continuant
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
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])
annotated source: continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

occurrent
type: Class
subclass of: entity
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
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.
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
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])
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.
BFO CLIF specification label: Occurrent
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.
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])
BFO OWL specification label: occurrent
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
editor preferred term: occurrent

Axiom
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])
annotated source: occurrent
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

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

Axiom
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.
annotated source: occurrent
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

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

Axiom
comment: per discussion with Barry Smith
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.
annotated source: occurrent
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006

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

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

independent continuant
type: Class
subclass of: continuant
BFO CLIF specification label: IndependentContinuant
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): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
BFO OWL specification label: ic
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]
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
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
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])
editor preferred term: independent continuant
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth

Axiom
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]
annotated source: independent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

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

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

Axiom
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])
annotated source: independent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
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])
annotated source: independent continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
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])
annotated source: independent continuant
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

obsolete dependent continuant
type: Class
subclass of: ObsoleteClass
deprecated: true
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
editor preferred term: obsolete dependent continuant

spatial region
type: Class
subclass of: immaterial entity
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
BFO OWL specification label: s-region
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.
BFO CLIF specification label: SpatialRegion
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]
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])
editor preferred term: spatial region

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

Axiom
comment: per discussion with Barry Smith
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.
annotated source: spatial region
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002

Axiom
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])
annotated source: spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

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

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

temporal region
type: Class
subclass of: occurrent
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
BFO CLIF specification label: TemporalRegion
BFO OWL specification label: t-region
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]
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])
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
editor preferred term: temporal region

Axiom
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
comment: per discussion with Barry Smith
annotated source: temporal region
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003

Axiom
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])
annotated source: temporal region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

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

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

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

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

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

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

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

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

spatiotemporal region
type: Class
subclass of: occurrent
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 (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
BFO OWL specification label: st-region
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
BFO CLIF specification label: SpatiotemporalRegion
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) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [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])
editor preferred term: spatiotemporal region
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

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

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

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

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

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

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

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

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

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

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

process
type: Class
subclass of: occurrent
BFO CLIF specification label: Process
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]
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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)
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
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])
BFO OWL specification label: process
editor preferred term: process
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.

Axiom
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]
annotated source: process
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
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])
annotated source: process
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
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]
BFO CLIF specification label: Disposition
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]
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.
BFO OWL specification label: disposition
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])
example of usage: an atom of element X has the disposition to decay to an atom of element Y
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])
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
editor preferred term: disposition
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis

Axiom
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]
annotated source: disposition
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
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])
annotated source: disposition
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
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]
annotated source: disposition
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
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])
annotated source: disposition
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
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]
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]
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.
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])
BFO CLIF specification label: RealizableEntity
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])
BFO OWL specification label: realizable
editor preferred term: realizable entity
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

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

Axiom
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]
annotated source: realizable entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
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])
annotated source: realizable entity
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
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]
annotated source: realizable entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

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

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

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

quality
type: Class
subclass of: specifically dependent continuant
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
BFO OWL specification label: quality
BFO CLIF specification label: Quality
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]
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])
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])
editor preferred term: 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

Axiom
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])
annotated source: quality
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
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]
annotated source: quality
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
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])
annotated source: quality
annotated property: has associated axiom(nl)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

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

specifically dependent continuant
type: Class
subclass of: continuant
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]
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]
definition: 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.
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
BFO CLIF specification label: SpecificallyDependentContinuant
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.
BFO OWL specification label: sdc
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])
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.
editor preferred term: specifically dependent continuant
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

Axiom
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])
annotated source: specifically dependent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
comment: per discussion with Barry Smith
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.
annotated source: specifically dependent continuant
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005

Axiom
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]
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
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]
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
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])
annotated source: specifically dependent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

role
type: Class
subclass of: realizable entity
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.
BFO CLIF specification label: Role
BFO OWL specification label: role
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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.
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.
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])
editor preferred term: role
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

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

Axiom
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])
annotated source: role
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object
type: Class
subclass of: material entity
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
BFO OWL specification label: fiat-object
BFO CLIF specification label: FiatObjectPart
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]
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])
editor preferred term: fiat object
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

Axiom
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])
annotated source: fiat object
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
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]
annotated source: fiat object
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
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])
BFO CLIF specification label: OneDimensionalSpatialRegion
BFO OWL specification label: 1d-s-region
example of usage: an edge of a cube-shaped portion of space.
editor preferred term: one-dimensional spatial region

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

Axiom
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])
annotated source: one-dimensional spatial region
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO CLIF specification label: ObjectAggregate
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.
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]
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: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
BFO OWL specification label: object-aggregate
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)
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])
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined via attributive delimitations such as: the patients in this hospital
editor preferred term: object aggregate
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.

Axiom
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])
annotated source: object aggregate
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
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.
annotated source: object aggregate
annotated property: definition source
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
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
annotated source: object aggregate
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
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
annotated source: object aggregate
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
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]
annotated source: object aggregate
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

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

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

Axiom
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
annotated source: three-dimensional spatial region
annotated property: elucidation
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
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
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
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])
editor preferred term: site
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)

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

Axiom
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])
annotated source: site
annotated property: elucidation
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
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
example of usage: atom
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])
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
editor preferred term: object
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star

Axiom
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])
annotated source: object
annotated property: elucidation
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
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
BFO CLIF specification label: GenericallyDependentContinuant
definition: 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.
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.
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])
editor preferred term: generically dependent continuant
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.

Axiom
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])
annotated source: generically dependent continuant
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

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

function
type: Class
subclass of: disposition
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
BFO CLIF specification label: Function
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])
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.
BFO OWL specification label: function
editor preferred term: 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

Axiom
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])
annotated source: function
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

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

process boundary
type: Class
subclass of: occurrent
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]
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
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])
editor preferred term: process boundary
example of usage: the boundary between the 2nd and 3rd year of your life.

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

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

Axiom
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]
annotated source: process boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
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])
annotated source: process boundary
annotated property: definition
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
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
BFO CLIF specification label: OneDimensionalTemporalRegion
BFO OWL specification label: 1d-t-region
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
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).
editor preferred term: one-dimensional temporal region
example of usage: the temporal region during which a process occurs.

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

Axiom
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
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
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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
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]
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])
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.
BFO CLIF specification label: MaterialEntity
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
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])
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
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])
editor preferred term: material entity
example of usage: the undetached arm of a human being

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

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

Axiom
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]
annotated source: material entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
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])
annotated source: material entity
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
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]
annotated source: material entity
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

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

continuant fiat boundary
type: Class
subclass of: immaterial entity
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.
BFO CLIF specification label: ContinuantFiatBoundary
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]
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
BFO OWL specification label: cf-boundary
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
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 preferred term: continuant fiat boundary

Axiom
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])
annotated source: continuant fiat boundary
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
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]
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
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.
annotated source: continuant fiat boundary
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
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
BFO CLIF specification label: ImmaterialEntity
editor preferred term: immaterial entity

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
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]
BFO OWL specification label: 1d-cf-boundary
example of usage: The Equator
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])
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
editor preferred term: one-dimensional continuant fiat boundary
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

Axiom
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])
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
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]
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
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
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]
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.
BFO CLIF specification label: ProcessProfile
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])
editor preferred term: process profile

Axiom
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]
annotated source: process profile
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

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

Axiom
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])
annotated source: process profile
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
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])
annotated source: process profile
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
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.
BFO OWL specification label: r-quality
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]
BFO CLIF specification label: RelationalQuality
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])
editor preferred term: relational quality

Axiom
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]
annotated source: relational quality
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
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])
annotated source: relational quality
annotated property: definition
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
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]
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
BFO OWL specification label: 2d-cf-boundary
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])
editor preferred term: two-dimensional continuant fiat boundary

Axiom
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])
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
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]
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
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]
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
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])
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.
editor preferred term: zero-dimensional continuant fiat boundary

Axiom
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]
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
comment: requested by Melanie Courtot
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.
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001

Axiom
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])
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
BFO CLIF specification label: ZeroDimensionalTemporalRegion
BFO OWL specification label: 0d-t-region
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
alternative term: temporal instant.
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.
editor preferred term: zero-dimensional temporal region

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

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

history
type: Class
subclass of: process
BFO OWL 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])
BFO CLIF specification label: History
editor preferred term: history

Axiom
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])
annotated source: history
annotated property: elucidation
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

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

biotin
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
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.
editor preferred term: biotin
imported from: chebi.owl

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

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

hydrogensulfite
type: Class
subclass of: molecular entity
definition: A sulfur oxoanion that has formula HO3S.
editor preferred term: hydrogensulfite
imported from: chebi.owl

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

molecular entity
type: Class
subclass of: material 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 preferred term: molecular 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

N-ethyl-N-nitrosourea
type: Class
subclass of: molecular entity
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.
editor preferred term: N-ethyl-N-nitrosourea
imported from: chebi.owl

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

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

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

lead(0)
type: Class
subclass of: molecular entity
definition: An elemental lead that has formula Pb.
editor preferred term: lead(0)
imported from: chebi.owl

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

hydroxyl
type: Class
subclass of: molecular entity
definition: An oxygen radical that has formula HO.
editor preferred term: hydroxyl
imported from: chebi.owl

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

ruthenium atom
type: Class
subclass of: molecular entity
definition: An iron group element atom that has formula Ru.
editor preferred term: ruthenium atom
imported from: chebi.owl

fluorescein
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
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.
editor preferred term: fluorescein
imported from: chebi.owl

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

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

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

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

atom
type: Class
subclass of: material entity
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
editor preferred term: atom
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
definition: A cobalt group element atom that has formula Rh.
editor preferred term: rhodium atom
imported from: chebi.owl

gadolinium atom
type: Class
subclass of: molecular entity
definition: A lanthanoid atom that has formula Gd.
editor preferred term: gadolinium atom
imported from: chebi.owl

terbium atom
type: Class
subclass of: molecular entity
definition: A lanthanoid atom that has formula Tb.
editor preferred term: terbium atom
imported from: chebi.owl

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

ribonucleic acid
type: Class
subclass of: nucleic 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.
editor preferred term: ribonucleic acid
imported from: chebi.owl

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

macromolecule
type: Class
subclass of: molecular entity
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.
editor preferred term: macromolecule
alternative term: polymer
imported from: chebi.owl

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

gadodiamide
type: Class
subclass of: molecular entity
definition: A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
editor preferred term: gadodiamide
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: Restriction
  on property: has role
  some values from: REO_0000171
definition: The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
editor preferred term: phosphorus-32 atom
imported from: chebi.owl

phosphorus-33 atom
type: Class
subclass of: atom
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
definition: The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
editor preferred term: phosphorus-33 atom
imported from: chebi.owl

Cy3 dye
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
editor preferred term: Cy3 dye
imported from: chebi.owl

Cy5 dye
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
editor preferred term: Cy5 dye
imported from: chebi.owl

digoxigenin
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
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.
editor preferred term: digoxigenin
imported from: chebi.owl

ethylenediaminetetraacetic acid
type: Class
subclass of: molecular entity
definition: A polyamino carboxylic acid that has formula C10H16N2O8.
editor preferred term: ethylenediaminetetraacetic acid
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

chromium-51
type: Class
subclass of: molecular entity
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.
editor preferred term: chromium-51
imported from: chebi.owl

Alexa Fluor 532
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
editor preferred term: Alexa Fluor 532
definition: An organosulfonic acid that has formula C34H33N3O11S2.
imported from: chebi.owl

Alexa Fluor 546
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
editor preferred term: Alexa Fluor 546
definition: An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3.
imported from: chebi.owl

Alexa Fluor 555
type: Class
subclass of: REO_0000280
subclass of: Restriction
  on property: has role
  some values from: REO_0000171
definition: A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
editor preferred term: Alexa Fluor 555
imported from: chebi.owl

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

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

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

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

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

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

fluorescence microscopy
type: Class
subclass of: OBI_0002119
definition: Any type of microscopy where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
alternative term: FM
alternative term: fluorescence imaging
alternative term: fluorescence microscopic imaging
editor preferred term: fluorescence microscopy
definition source: CHMO

confocal fluorescence microscopy
type: Class
subclass of: OBI_0002119
alternative term: CLSM
alternative term: LSCM
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 term: confocal fluorescence imaging
alternative term: confocal fluorescence microscopy
editor preferred term: confocal fluorescence microscopy
alternative term: confocal laser scanning fluorescence microscopy
alternative term: confocal laser scanning microscopy
alternative term: confocal-laser scanning microscopy
alternative term: fluorescence confocal microscopy
alternative term: fluorescence confocal scanning laser microscopy
alternative term: scanning confocal fluorescence microscopy
definition source: CHMO

light microscopy
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 term: OM
alternative term: light microscopy
editor preferred term: light microscopy
alternative term: optical microscopy
definition source: CHMO

liquid chromatography-tandem mass spectrometry
type: Class
subclass of: OBI_0200198
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 term: LC-MS-MS
alternative term: LC-MS/MS
alternative term: LC-MS2
alternative term: LC-MSMS
alternative term: LC/MS/MS
alternative term: LCMSMS
alternative term: liquid chromatography tandem mass spectrometry
alternative term: liquid chromatography tandem mass spectroscopy
editor preferred term: liquid chromatography-tandem mass spectrometry
alternative term: liquid chromatography-tandem mass spectroscopy
definition source: CHMO

cell line cell
type: Class
subclass of: OBI_0001866
subclass of: Restriction
  on property: derives from
  some values from: primary cultured cell
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
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
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.
annotated source: cell line cell
annotated property: subClassOf
annotated target: Restriction
  on property: derives from
  some values from: primary cultured cell

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
  all values from: cell line cell
subclass of: Restriction
  on property: has grain
  some values from: cell line cell
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).
editor preferred term: cell line
imported from: clo.owl

immortal cell line
type: Class
subclass of: cell line
subclass of: Restriction
  on property: has grain
  all values from: immortal cell line cell
subclass of: Restriction
  on property: has grain
  some values from: immortal cell line cell
definition: A cell line that is expected to be capable of indefinite propagation in an vitro culture.
editor preferred term: immortal cell line
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
  on class: cell line immortalization
  qualified cardinality: 0
definition: A cell line is able to support only a limited number of passages in vitro.
editor preferred term: mortal cell line
imported from: clo.owl

cell
type: Class
subclass of: material entity
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.
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 .."
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
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.
editor preferred term: primary cultured cell
imported from: cl.owl

native cell
type: Class
subclass of: cell
definition: 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).
editor preferred term: native cell
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
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
editor preferred term: cultured cell
imported from: cl.owl

fibroblast
type: Class
subclass of: cell
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.
editor preferred term: fibroblast
imported from: cl.owl

epithelial cell
type: Class
subclass of: 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.
editor preferred term: epithelial cell
imported from: cl.owl

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

mast cell
type: Class
subclass of: 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.
editor preferred term: mast cell
imported from: cl.owl

hepatocyte
type: Class
subclass of: epithelial cell
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.
editor preferred term: hepatocyte
imported from: cl.owl

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

macrophage
type: Class
subclass of: cell
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.
editor preferred term: macrophage
imported from: cl.owl

B cell
type: Class
subclass of: lymphocyte
definition: A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
editor preferred term: B cell
imported from: cl.owl

dendritic cell
type: Class
subclass of: 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).
editor preferred term: dendritic cell
imported from: cl.owl

lymphocyte
type: Class
subclass of: mononuclear cell
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.
editor preferred term: lymphocyte
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
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
editor preferred term: experimentally modified cell in vitro
imported from: cl.owl

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

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

basophil
type: Class
subclass of: cell
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.
editor preferred term: basophil
imported from: cl.owl

plasma cell
type: Class
subclass of: B 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.
editor preferred term: plasma cell
imported from: cl.owl

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

CD8-positive, alpha-beta cytotoxic T cell
type: Class
subclass of: CD8-positive, alpha-beta 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.
editor preferred term: CD8-positive, alpha-beta cytotoxic T cell
imported from: cl.owl

mature NK T cell
type: Class
subclass of: alpha-beta 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.
editor preferred term: mature NK T cell
imported from: cl.owl

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

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

podzol
type: Class
subclass of: soil
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.
editor preferred term: podzol
imported from: envo.owl

environmental material
type: Class
subclass of: material entity
definition: A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
editor preferred term: environmental material
imported from: envo.owl

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

core promoter binding
type: Class
subclass of: binding
definition: Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
editor preferred term: core promoter binding
imported from: go.owl

antibody-dependent cellular cytotoxicity
type: Class
subclass of: biological_process
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.
editor preferred term: antibody-dependent cellular cytotoxicity
imported from: go.owl

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

cytokine production
type: Class
subclass of: biological_process
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.
editor preferred term: cytokine production
imported from: go.owl

cell killing
type: Class
subclass of: biological_process
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.
editor preferred term: cell killing
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

adaptive immune response
type: Class
subclass of: immune response
definition: An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
editor preferred term: adaptive immune response
imported from: go.owl

cytokine production involved in immune response
type: Class
subclass of: cytokine production
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.
editor preferred term: cytokine production involved in immune response
imported from: go.owl

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

tolerance induction
type: Class
subclass of: biological_process
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.
editor preferred term: tolerance induction
imported from: go.owl

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

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

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

cytokine production involved in inflammatory response
type: Class
subclass of: cytokine production
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.
editor preferred term: cytokine production involved in inflammatory response
imported from: go.owl

molecular_function
type: Class
subclass of: function
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
editor preferred term: molecular_function
imported from: go.owl

antigen binding
type: Class
subclass of: process
definition: Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
editor preferred term: antigen binding
imported from: go.owl

catalytic activity
type: Class
subclass of: molecular_function
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.
editor preferred term: catalytic activity
imported from: go.owl

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

ion channel activity
type: Class
subclass of: cellular process
definition: Catalysis of facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
editor preferred term: ion channel activity
imported from: go.owl

cellular_component
type: Class
subclass of: material entity
definition: The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
editor preferred term: cellular_component
imported from: go.owl

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

mitochondrion
type: Class
subclass of: membrane-bounded organelle
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.
editor preferred term: mitochondrion
imported from: go.owl

glucose metabolic process
type: Class
subclass of: biological_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.
editor preferred term: glucose metabolic process
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 initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
imported from: go.owl

DNA methylation
type: Class
subclass of: biological_process
editor preferred term: DNA methylation
definition: The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
imported from: go.owl

chromatin remodeling
type: Class
subclass of: cellular process
definition: Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
editor preferred term: chromatin remodeling
imported from: go.owl

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

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

cellular response to DNA damage stimulus
type: Class
subclass of: response to stimulus
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.
editor preferred term: cellular response to DNA damage stimulus
imported from: go.owl

cell cycle
type: Class
subclass of: biological_process
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.
editor preferred term: cell cycle
imported from: go.owl

blood coagulation
type: Class
subclass of: biological_process
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.
editor preferred term: blood coagulation
imported from: go.owl

biological_process
type: Class
subclass of: process
disjoint with: planned process
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
editor preferred term: biological_process
imported from: go.owl

opsonization
type: Class
subclass of: phagocytosis
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.
editor preferred term: opsonization
imported from: go.owl

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

fertilization
type: Class
subclass of: biological_process
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).
editor preferred term: fertilization
imported from: go.owl

cellular process
type: Class
subclass of: biological_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.
editor preferred term: cellular process
imported from: go.owl

gene expression
type: Class
subclass of: biological_process
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
editor preferred term: gene expression
imported from: go.owl

vascular endothelial growth factor production
type: Class
subclass of: cytokine 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.
editor preferred term: vascular endothelial growth factor production
imported from: go.owl

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

histone modification
type: Class
subclass of: biological_process
definition: The covalent alteration of one or more amino acid residues within a histone protein.
editor preferred term: histone modification
imported from: go.owl

immunoglobulin complex
type: Class
subclass of: protein 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.
editor preferred term: immunoglobulin complex
imported from: go.owl

B cell receptor complex
type: Class
subclass of: OBI_1110022
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.
editor preferred term: B cell receptor complex
imported from: go.owl

antigen processing and presentation
type: Class
subclass of: biological_process
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.
editor preferred term: antigen processing and presentation
imported from: go.owl

protein domain specific binding
type: Class
subclass of: binding
definition: Interacting selectively and non-covalently with a specific domain of a protein.
editor preferred term: protein domain specific binding
imported from: go.owl

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

hemopoiesis
type: Class
subclass of: biological_process
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.
editor preferred term: hemopoiesis
imported from: go.owl

connective tissue growth factor production
type: Class
subclass of: cytokine 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.
editor preferred term: connective tissue growth factor production
imported from: go.owl

chemokine production
type: Class
subclass of: cytokine 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.
editor preferred term: chemokine production
imported from: go.owl

granulocyte macrophage colony-stimulating factor production
type: Class
subclass of: cytokine 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.
editor preferred term: granulocyte macrophage colony-stimulating factor production
imported from: go.owl

hepatocyte growth factor production
type: Class
subclass of: cytokine 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.
editor preferred term: hepatocyte growth factor production
imported from: go.owl

type I interferon production
type: Class
subclass of: cytokine 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.
editor preferred term: type I interferon production
imported from: go.owl

interferon-beta production
type: Class
subclass of: cytokine 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.
editor preferred term: interferon-beta production
imported from: go.owl

interferon-gamma production
type: Class
subclass of: cytokine 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.
editor preferred term: interferon-gamma production
imported from: go.owl

interleukin-1 alpha production
type: Class
subclass of: interleukin-1 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.
editor preferred term: interleukin-1 alpha production
imported from: go.owl

interleukin-1 beta production
type: Class
subclass of: interleukin-1 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.
editor preferred term: interleukin-1 beta production
imported from: go.owl

interleukin-1 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-1 production
imported from: go.owl

interleukin-10 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-10 production
imported from: go.owl

interleukin-11 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-11 production
imported from: go.owl

interleukin-12 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-12 production
imported from: go.owl

interleukin-13 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-13 production
imported from: go.owl

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

interleukin-15 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-15 production
imported from: go.owl

interleukin-16 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-16 production
imported from: go.owl

interleukin-17 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-17 production
imported from: go.owl

interleukin-18 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-18 production
imported from: go.owl

interleukin-19 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-19 production
imported from: go.owl

interleukin-2 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-2 production
imported from: go.owl

interleukin-20 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-20 production
imported from: go.owl

interleukin-21 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-21 production
imported from: go.owl

interleukin-22 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-22 production
imported from: go.owl

interleukin-23 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-23 production
imported from: go.owl

interleukin-24 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-24 production
imported from: go.owl

interleukin-25 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-25 production
imported from: go.owl

interleukin-26 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-26 production
imported from: go.owl

interleukin-27 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-27 production
imported from: go.owl

interleukin-3 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-3 production
imported from: go.owl

interleukin-4 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-4 production
imported from: go.owl

interleukin-5 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-5 production
imported from: go.owl

interleukin-6 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-6 production
imported from: go.owl

interleukin-7 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-7 production
imported from: go.owl

interleukin-8 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-8 production
imported from: go.owl

interleukin-9 production
type: Class
subclass of: cytokine 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.
editor preferred term: interleukin-9 production
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
alternative term: TNF alpha 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.
editor preferred term: tumor necrosis factor production
imported from: go.owl

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

transforming growth factor beta1 production
type: Class
subclass of: cytokine 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.
editor preferred term: transforming growth factor beta1 production
imported from: go.owl

transforming growth factor beta2 production
type: Class
subclass of: cytokine 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.
editor preferred term: transforming growth factor beta2 production
imported from: go.owl

transforming growth factor beta3 production
type: Class
subclass of: cytokine 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.
editor preferred term: transforming growth factor beta3 production
imported from: go.owl

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

DNA polymerase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
editor preferred term: DNA polymerase activity
imported from: go.owl

type III interferon production
type: Class
subclass of: cytokine 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.
editor preferred term: type III interferon production
imported from: go.owl

chemokine (C-X-C motif) ligand 9 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-X-C motif) ligand 9 production
imported from: go.owl

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

granzyme A production
type: Class
subclass of: biological_process
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.
editor preferred term: granzyme A production
imported from: go.owl

perforin production
type: Class
subclass of: biological_process
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.
editor preferred term: perforin production
imported from: go.owl

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

regulation of gene expression, epigenetic
type: Class
subclass of: regulation of molecular function, epigenetic
definition: Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
editor preferred term: regulation of gene expression, epigenetic
imported from: go.owl

regulation of molecular function, epigenetic
type: Class
subclass of: biological_process
definition: Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
editor preferred term: regulation of molecular function, epigenetic
imported from: go.owl

T cell proliferation
type: Class
subclass of: cell 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
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.
editor preferred term: T cell receptor complex
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
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.
IEDB alternative term: antibody
alternative term: antibody
editor preferred term: immunoglobulin complex, circulating
imported from: go.owl

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

peptide antigen binding
type: Class
subclass of: antigen binding
definition: Interacting selectively and non-covalently with an antigen peptide.
editor preferred term: peptide antigen binding
imported from: go.owl

MHC protein complex
type: Class
subclass of: 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.
editor preferred term: MHC protein complex
imported from: go.owl

membrane-bounded organelle
type: Class
subclass of: cellular_component
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.
editor preferred term: membrane-bounded organelle
imported from: go.owl

protein complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: PR_000000001
example of usage: A ribosome is a protein complex
definition: Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
editor preferred term: protein complex
imported from: go.owl

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

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

regulation of DNA methylation
type: Class
subclass of: regulation of molecular function, epigenetic
definition: Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
editor preferred term: regulation of DNA methylation
imported from: go.owl

macrophage migration inhibitory factor production
type: Class
subclass of: cytokine 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.
editor preferred term: macrophage migration inhibitory factor production
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
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.
editor preferred term: chemokine (C-C motif) ligand 17 production
imported from: go.owl

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

response to stimulus
type: Class
subclass of: biological_process
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.
editor preferred term: response to stimulus
imported from: go.owl

chromosome organization
type: Class
subclass of: biological_process
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.
editor preferred term: chromosome organization
imported from: go.owl

actin polymerization-dependent cell motility
type: Class
subclass of: biological_process
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.
editor preferred term: actin polymerization-dependent cell motility
imported from: go.owl

transforming growth factor beta production
type: Class
subclass of: cytokine 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.
editor preferred term: transforming growth factor beta production
imported from: go.owl

monocyte chemotactic protein-1 production
type: Class
subclass of: chemokine 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.
editor preferred term: monocyte chemotactic protein-1 production
imported from: go.owl

chemokine (C-C motif) ligand 4 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-C motif) ligand 4 production
imported from: go.owl

macrophage inflammatory protein-1 gamma production
type: Class
subclass of: chemokine 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.
editor preferred term: macrophage inflammatory protein-1 gamma production
imported from: go.owl

macrophage inflammatory protein-1 alpha production
type: Class
subclass of: chemokine 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.
editor preferred term: macrophage inflammatory protein-1 alpha production
imported from: go.owl

chemokine (C-C motif) ligand 5 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-C motif) ligand 5 production
imported from: go.owl

chemokine (C-C motif) ligand 1 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-C motif) ligand 1 production
imported from: go.owl

granulocyte colony-stimulating factor production
type: Class
subclass of: cytokine 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.
editor preferred term: granulocyte colony-stimulating factor production
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
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.
editor preferred term: granzyme B production
imported from: go.owl

tumor necrosis factor superfamily cytokine production
type: Class
subclass of: 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.
editor preferred term: tumor necrosis factor superfamily cytokine production
imported from: go.owl

chemokine (C-C motif) ligand 22 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-C motif) ligand 22 production
imported from: go.owl

tumor necrosis factor (ligand) superfamily member 11 production
type: Class
subclass of: tumor necrosis factor superfamily cytokine 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.
editor preferred term: tumor necrosis factor (ligand) superfamily member 11 production
imported from: go.owl

interleukin-17A production
type: Class
subclass of: interleukin-17 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.
editor preferred term: interleukin-17A production
imported from: go.owl

interleukin-17F production
type: Class
subclass of: interleukin-17 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.
editor preferred term: interleukin-17F production
imported from: go.owl

complement-dependent cytotoxicity
type: Class
subclass of: cell killing
definition: Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody.
editor preferred term: complement-dependent cytotoxicity
imported from: go.owl

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

immune complex formation
type: Class
subclass of: immunoglobulin mediated immune response
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.
editor preferred term: immune complex formation
imported from: go.owl

immunoglobulin-mediated neutralization
type: Class
subclass of: immunoglobulin mediated immune response
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.
editor preferred term: immunoglobulin-mediated neutralization
imported from: go.owl

chemokine (C-C motif) ligand 19 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-C motif) ligand 19 production
imported from: go.owl

chemokine (C-C motif) ligand 21 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-C motif) ligand 21 production
imported from: go.owl

chemokine (C-X-C motif) ligand 12 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-X-C motif) ligand 12 production
imported from: go.owl

chemokine (C-X-C motif) ligand 13 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-X-C motif) ligand 13 production
imported from: go.owl

chemokine (C-X-C motif) ligand 16 production
type: Class
subclass of: chemokine 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.
editor preferred term: chemokine (C-X-C motif) ligand 16 production
imported from: go.owl

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

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI branch derived
definition source: OBI_0000349
term editor: PlanAndPlannedProcess Branch
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
editor preferred term: conditional specification
has curation status: IAO_0000120

measurement unit label
type: Class
subclass of: datum label
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor preferred term: measurement unit label
has curation status: IAO_0000125

objective specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
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.
alternative term: goal specification
editor preferred term: objective specification
has curation status: IAO_0000122

narrative object
type: Class
subclass of: information content entity
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition: A narrative object is an information content entity that is a set of propositions.
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
definition source: OBI_0000013
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition source: group:OBI
editor preferred term: narrative object
term editor: person:Chris Stoeckert
has curation status: IAO_0000123

action specification
type: Class
subclass of: directive information entity
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
editor preferred term: action specification
has curation status: IAO_0000122

obsolete_artifact
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_artifact
deprecated: true
has obsolescence reason: IAO_0000103

datum label
type: Class
subclass of: information content entity
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
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
term editor: GROUP: IAO
editor preferred term: datum label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
has curation status: IAO_0000123

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
editor preferred term: software
has curation status: IAO_0000120

obsolete2_digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000261
deprecated: true
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
definition: A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
definition source: group:OBI
editor preferred term: obsolete2_digital entity
term editor: person:Chris Stoeckert
has obsolescence reason: IAO_0000103

journal article
type: Class
subclass of: report
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
definition source: OBI_0000159
definition: a report that is published in a journal
definition source: group:OBI
editor preferred term: journal article
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
has curation status: IAO_0000120

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
definition: A quality of an information bearer that imparts the information content
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
editor preferred term: information carrier
has curation status: IAO_0000125

model number
type: Class
subclass of: symbol
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: Person: Alan Ruttenberg
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
editor preferred term: model number
has curation status: IAO_0000125

obsolete_material_entity
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_material_entity
deprecated: true
has obsolescence reason: IAO_0000226

obsolete2_binary digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000244
deprecated: true
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
definition: A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
example of usage: MS Word document, ZIP file, DICOM file, JPEG file
editor note: digital_entity
definition source: group:OBI
editor preferred term: obsolete2_binary digital entity
term editor: person:Chris Stoeckert
has obsolescence reason: IAO_0000103

obsolete_unit of measure
type: Class
subclass of: ObsoleteClass
term editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The length of a ruler.
definition: a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
editor preferred term: obsolete_unit of measure
deprecated: true
has obsolescence reason: IAO_0000103

programming language
type: Class
subclass of: plan specification
definition: A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition source: OBI_0000058
example of usage: R, Perl, Java
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: programming language
has curation status: IAO_0000120

data item
type: Class
subclass of: information content entity
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
definition: a data item is 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.
alternative term: data
editor preferred term: data item
has curation status: IAO_0000125

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
editor note: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
term editor: PERSON: James A. Overton
term editor: PERSON: Jonathan Rees
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
definition source: based on Oxford English Dictionary
editor preferred term: symbol
has curation status: IAO_0000125

numeral
type: Class
subclass of: symbol
definition: A symbol that denotes a number.
term editor: PERSON: Jonathan Rees
editor preferred term: numeral
has curation status: IAO_0000123

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
definition: A generically dependent continuant that is about some thing.
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
term editor: PERSON: Chris Stoeckert
editor preferred term: information content entity
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
has curation status: IAO_0000122

integer numeral
type: Class
subclass of: numeral
term editor: PERSON: Jonathan Rees
definition: a numeral that denotes an integer
editor preferred term: integer numeral
has curation status: IAO_0000123

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001931
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
example of usage: 10 feet. 3 ml.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor preferred term: scalar measurement datum
has curation status: IAO_0000120

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
editor preferred term: directive information entity
has curation status: IAO_0000122

time trigger
type: Class
subclass of: conditional specification
definition source: OBI branch derived
definition source: OBI_0000331
term editor: PlanAndPlannedProcess Branch
definition: revisit?
editor preferred term: time trigger
has curation status: IAO_0000124

obsolete_study interpretation
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
editor 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 this definition please notify OBI.
definition source: OBI_0000005
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
alternative term: conclusion
deprecated: true
definition: A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
term editor: Lawrence Hunter
term editor: PERSON: Jennifer Fostel
editor note: The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
editor preferred term: obsolete_study interpretation
has obsolescence reason: IAO_0000103
has curation status: IAO_0000125

dot plot
type: Class
subclass of: graph
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.
example of usage: Dot plot of SSC-H and FSC-H.
definition source: OBI_0000123
editor preferred term: dot plot
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000002

graph
type: Class
subclass of: diagram
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.
definition source: OBI_0000240
term editor: PERSON: Lawrence Hunter
editor preferred term: graph
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
has curation status: IAO_0000125

obsolete2_text based digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000132
definition source: group:OBI
deprecated: true
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
definition: A text based digital entity is a digital entity that is encoded so that it only contains text characters.
example of usage: XML file, C++ source code file
editor note: digital_entity
editor preferred term: obsolete2_text based digital entity
term editor: person:Chris Stoeckert
has obsolescence reason: IAO_0000103

rule
type: Class
subclass of: conditional specification
editor note: MSI
definition source: OBI_0500021
term editor: PRS
definition source: PRS
definition: a rule is an executable which guides, defines, restricts actions
example of usage: example to be added
editor preferred term: rule
has curation status: IAO_0000123

contour plot
type: Class
subclass of: graph
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
definition source: OBI_0000246
editor preferred term: contour plot
editor note: generically_dependent_continuants
definition source: group:Flow Cytometry community
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000002

obsolete2_report figure
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000027
deprecated: true
definition: A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
editor note: I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
editor note: Replaced by defined version of figure
definition source: group:OBI
editor preferred term: obsolete2_report figure
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
has obsolescence reason: IAO_0000103
has curation status: IAO_0000124

algorithm
type: Class
subclass of: plan specification
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.
definition source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: IAO_0000120

software interpreter
type: Class
subclass of: algorithm
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition source: OBI_0000199
example of usage: R program, Perl interpreter, Java virtual machine
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: software interpreter
has curation status: IAO_0000120

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000002
  one of: IAO_0000124
  one of: IAO_0000125
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000428
  one of: IAO_0000423
subclass of: data about an ontology part
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
term editor: PERSON:Bill Bug
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 preferred term: curation status specification
has curation status: IAO_0000125

density plot
type: Class
subclass of: graph
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.
example of usage: Density plot of SSC-H and FSC-H.
definition source: OBI_0000179
editor preferred term: density plot
definition source: group:Flow Cytometry community
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000002

report
type: Class
subclass of: document
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor 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 this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
definition source: GROUP: OBI
definition source: OBI_0000099
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term editor: PERSON:Chris Stoeckert
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)
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
editor preferred term: report
has curation status: IAO_0000125

obsolete_report element
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: needs some more work (clarify relations).
editor note: 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
editor 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 this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000001
term editor: PERSON: Melanie Courtot
editor note: Replaced by textual entity and figure
deprecated: true
definition: A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
definition source: GROUP:OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Allyson Lister
editor note: There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
editor preferred term: obsolete_report element
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

obsolete2_binary executable
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000222
deprecated: true
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'
definition: Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
definition source: group:OBI
editor preferred term: obsolete2_binary executable
term editor: person:Jennifer Fostel
has obsolescence reason: IAO_0000103

source code module
type: Class
subclass of: directive information entity
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition source: OBI_0000039
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: source code module
has curation status: IAO_0000123

obsolete_report table
type: Class
subclass of: ObsoleteClass
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000265
deprecated: true
definition: A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
definition source: group:OBI
editor preferred term: obsolete_report table
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
has curation status: IAO_0000002
has obsolescence reason: IAO_0000103

data format specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
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
definition source: OBI branch derived
definition source: OBI_0000187
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: IAO_0000123

data set
type: Class
subclass of: data item
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
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.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
definition source: OBI_0000042
editor preferred term: data set
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

image
type: Class
subclass of: figure
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.
definition source: OBI_0000030
definition source: group:OBI
editor preferred term: image
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
has curation status: IAO_0000122

data about an ontology part
type: Class
subclass of: data item
term editor: Person:Alan Ruttenberg
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

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
term editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
editor preferred term: plan specification
has curation status: IAO_0000122

obsolete2_digital document
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000195
deprecated: true
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
definition: A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
definition source: group:OBI
editor preferred term: obsolete2_digital document
term editor: person:Jennifer Fostel
has obsolescence reason: IAO_0000103

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001933
editor note: 2/2/2009 is_specified_output of some assay?
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.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred term: measurement datum
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

obsolete_identifier
type: Class
subclass of: ObsoleteClass
editor note: _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
editor preferred term: obsolete_identifier
deprecated: true
has curation status: IAO_0000121
has obsolescence reason: IAO_0000226

version number
type: Class
subclass of: symbol
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
term editor: GROUP: IAO
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
editor preferred term: version number
has curation status: IAO_0000123

serial number
type: Class
subclass of: symbol
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: GROUP: IAO
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
editor preferred term: serial number
has curation status: IAO_0000123

lot number
type: Class
subclass of: symbol
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
term editor: GROUP: IAO
alternative term: batch number
editor preferred term: lot number
has curation status: IAO_0000123

setting datum
type: Class
subclass of: data item
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
editor preferred term: setting datum
has curation status: IAO_0000123

obsolete_digital quality
type: Class
subclass of: ObsoleteClass
editor note: Need to rework digital entity. Digital quality was suggested by Barry.
editor preferred term: obsolete_digital quality
deprecated: true
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
has obsolescence reason: IAO_0000103

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: OBI_0001909
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
term editor: Person:Alan Ruttenberg
editor preferred term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: IAO_0000120

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
definition: A material entity in which a concretization of an information content entity inheres.
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
term editor: GROUP: IAO
example of usage: a brain
example of usage: a hard drive
editor preferred term: material information bearer
has curation status: IAO_0000122

histogram
type: Class
subclass of: graph
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition source: GROUP:OBI
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
editor preferred term: histogram
has curation status: IAO_0000122

heatmap
type: Class
subclass of: graph
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.
definition source: GROUP:OBI
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
editor preferred term: heatmap
has curation status: IAO_0000122

Venn diagram
type: Class
subclass of: graph
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
editor preferred term: Venn diagram
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram
has curation status: IAO_0000122

obsolete_survival curve
type: Class
subclass of: ObsoleteClass
deprecated: true
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
editor preferred term: obsolete_survival curve
has obsolescence reason: IAO_0000103
has curation status: IAO_0000122

dendrogram
type: Class
subclass of: graph
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.
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: dendrogram
has curation status: IAO_0000122

scatter plot
type: Class
subclass of: graph
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.
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
editor preferred term: scatter plot
alternative term: scattergraph
has curation status: IAO_0000122

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Joanne Luciano
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
editor preferred term: photograph
has curation status: IAO_0000122

photographic print
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: photograph
subclass of: material information bearer
definition: A photographic print is a material entity upon which a photograph generically depends.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred term: photographic print
has curation status: IAO_0000125

obsolescence reason specification
type: Class
equivalent class: Class
  one of: IAO_0000103
  one of: IAO_0000229
  one of: IAO_0000226
  one of: IAO_0000227
  one of: IAO_0000228
subclass of: data about an ontology part
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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 preferred term: obsolescence reason specification
has curation status: IAO_0000125

textual entity
type: Class
subclass of: information content 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.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
term editor: PERSON: Lawrence Hunter
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
alternative term: text
editor preferred term: textual entity
has curation status: IAO_0000123

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
term editor: PERSON: Lawrence Hunter
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication
editor preferred term: citation
has curation status: IAO_0000125

author identification
type: Class
subclass of: written name
definition: A textual entity intended to identify a particular author
example of usage: L. Hunter
term editor: PERSON: Lawrence Hunter
editor preferred term: author identification
has curation status: IAO_0000125

institutional identification
type: Class
subclass of: textual entity
definition: A textual entity intended to identify a particular institution
term editor: PERSON: Lawrence Hunter
example of usage: University of Colorado Denver School of Medicine
editor preferred term: institutional identification
has curation status: IAO_0000125

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
definition: A textual entity that describes a figure
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
term editor: PERSON: Lawrence Hunter
editor preferred term: caption
has curation status: IAO_0000125

document title
type: Class
subclass of: textual entity
definition: A textual entity that names a document
term editor: PERSON: Lawrence Hunter
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
editor preferred term: document title
has curation status: IAO_0000125

table
type: Class
subclass of: textual entity
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
term editor: PERSON: Lawrence Hunter
editor preferred term: table
example of usage: | T F --+----- T | T F F | F F
has curation status: IAO_0000125

table of abbreviations
type: Class
subclass of: table
definition: A table where the constituent texts are abbreviations and their expansions
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
term editor: PERSON: Lawrence Hunter
editor preferred term: table of abbreviations
has curation status: IAO_0000125

figure
type: Class
subclass of: information content entity
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
example of usage: Any picture, diagram or table
term editor: PERSON: Lawrence Hunter
editor preferred term: figure
has curation status: IAO_0000120

diagram
type: Class
subclass of: figure
definition: A figure that expresses one or more propositions
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
term editor: PERSON: Lawrence Hunter
editor preferred term: diagram
has curation status: IAO_0000120

document
type: Class
subclass of: information content entity
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
term editor: PERSON: Lawrence Hunter
editor preferred term: document
has curation status: IAO_0000120

publication
type: Class
subclass of: document
definition: A document that has been accepted by a publisher
example of usage: A journal article or book
term editor: PERSON: Lawrence Hunter
editor preferred term: publication
has curation status: IAO_0000120

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: investigation
definition: A publication that is about an investigation
example of usage: Most scientific journal articles
term editor: PERSON: Lawrence Hunter
editor preferred term: publication about an investigation
alternative term: scientific publication
has curation status: IAO_0000120

patent
type: Class
subclass of: document
definition: A document that has been accepted by a patent authority
term editor: PERSON: Lawrence Hunter
example of usage: US Patent 6,449,603
editor preferred term: patent
has curation status: IAO_0000120

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: document
example of usage: An abstract, introduction, method or results section.
term editor: PERSON: Lawrence Hunter
definition: an information content entity that is part of a document
editor preferred term: document part
has curation status: IAO_0000120

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
term editor: PERSON: Lawrence Hunter
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
editor preferred term: abstract
has curation status: IAO_0000120

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
term editor: PERSON: Lawrence Hunter
example of usage: Section labelled 'introduction' of a typical scientific journal article
alternative term: introduction
editor preferred term: introduction to a publication about an investigation
has curation status: IAO_0000120

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: OBI_0500000
definition: A part of a publication about an investigation that is about the study design of the investigation
term editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
editor preferred term: methods section
has curation status: IAO_0000120

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design execution
definition: A part of a publication about an investigation that is about a study design execution
term editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'results' in a typical scientific journal article
editor preferred term: results section
has curation status: IAO_0000120

discussion section of a publication about an investigation
type: Class
subclass of: document part
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
term editor: PERSON: Lawrence Hunter
alternative term: discussion section
editor preferred term: discussion section of a publication about an investigation
has curation status: IAO_0000120

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: citation
definition: A part of a document that has citations as parts
term editor: PERSON: Lawrence Hunter
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
editor preferred term: references section
has curation status: IAO_0000120

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author identification
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
term editor: PERSON: Lawrence Hunter
editor preferred term: author list
definition: part of a document that enumerates the authors of the document
has curation status: IAO_0000120

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: institutional identification
term editor: PERSON: Lawrence Hunter
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
editor preferred term: institution list
definition: part of a document that has parts that are institution identifications associated with the authors of the document
has curation status: IAO_0000120

author contributions section
type: Class
subclass of: document part
definition: A part of a publication that is about the specific contributions of each author
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
term editor: PERSON: Lawrence Hunter
editor preferred term: author contributions section
has curation status: IAO_0000120

acknowledgements section
type: Class
subclass of: document part
term editor: PERSON: Lawrence Hunter
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
editor preferred term: acknowledgements section
has curation status: IAO_0000120

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
term editor: PERSON: Lawrence Hunter
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
alternative term: endnote
editor preferred term: footnote
has curation status: IAO_0000120

supplementary material to a document
type: Class
subclass of: document part
term editor: PERSON: Lawrence Hunter
alternative term: appendix
definition: part of a document that is segregated from the rest of the document due to its size
alternative term: supplementary material
editor preferred term: supplementary material to a document
has curation status: IAO_0000120

table of contents
type: Class
subclass of: table
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
term editor: PERSON: Lawrence Hunter
editor preferred term: table of contents
has curation status: IAO_0000125

table of figures
type: Class
subclass of: table
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
term editor: PERSON: Lawrence Hunter
editor preferred term: table of figures
has curation status: IAO_0000125

running title
type: Class
subclass of: document title
definition: A shorter version of a document title
term editor: PERSON: Lawrence Hunter
editor preferred term: running title
has curation status: IAO_0000125

copyright section
type: Class
subclass of: document part
definition: A document part that describes legal restrictions on making or distributing copies of the document
term editor: PERSON: Lawrence Hunter
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
editor preferred term: copyright section
has curation status: IAO_0000120

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: zero-dimensional spatial region
curator note: AR notes: We need to discuss whether it should include site.
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
term editor: Alan Ruttenberg
editor preferred term: cartesian spatial coordinate datum
has curation status: IAO_0000120

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: one-dimensional spatial region
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
term editor: Alan Ruttenberg
editor preferred term: one dimensional cartesian spatial coordinate datum
has curation status: IAO_0000123

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: two-dimensional spatial region
definition: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
term editor: Alan Ruttenberg
editor preferred term: two dimensional cartesian spatial coordinate datum
has curation status: IAO_0000123

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: three-dimensional spatial region
definition: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
term editor: Alan Ruttenberg
editor preferred term: three dimensional cartesian spatial coordinate datum
has curation status: IAO_0000123

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0000122
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000001
definition: A scalar measurement datum that is the result of measurement of length quality
term editor: Alan Ruttenberg
editor preferred term: length measurement datum
has curation status: IAO_0000123

denotator type
type: Class
equivalent class: Class
  one of: IAO_0000420
  one of: IAO_0000410
  one of: IAO_0000421
subclass of: data about an ontology part
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
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.
editor preferred term: denotator type

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000002
  intersection of: Restriction
    on property: is quality measurement of
    all values from: PATO_0000125
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality
term editor: Person:Alan Ruttenberg
editor preferred term: mass measurement datum
has curation status: IAO_0000123

hypothesis textual entity
type: Class
subclass of: textual entity
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A textual entity that expresses an assertion that is intended to be tested.
term editor: Person:Alan Ruttenberg
editor preferred term: hypothesis textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: IAO_0000120

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000003
  intersection of: Restriction
    on property: is duration of
    all values from: process
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measuring a temporal interval
term editor: Person:Alan Ruttenberg
editor preferred term: time measurement datum
has curation status: IAO_0000123

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographic location
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59
editor preferred term: postal address
has curation status: IAO_0000123

email address
type: Class
subclass of: information content entity
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
editor preferred term: email address
has curation status: IAO_0000123

author role
type: Class
subclass of: role
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor preferred term: author role
has curation status: IAO_0000125

data item extraction from journal article
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: journal article
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
definition: a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
term editor: Person:Alan Ruttenberg
editor preferred term: data item extraction from journal article
has curation status: IAO_0000120

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
definition: a planned process in which a document is created or added to by including the specified input in it.
editor preferred term: documenting
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has curation status: IAO_0000125

line graph
type: Class
subclass of: graph
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition source: GROUP:OBI
term editor: PERSON:Chris Stoeckert
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
alternative term: line chart
editor preferred term: line graph
has curation status: IAO_0000122

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
subclass of: Restriction
  on property: has_specified_output
  some values from: centrally registered identifier symbol
editor note: 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
example of usage: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
term editor: Person:Melanie Courtot
alternative term: assigning a CRID
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
editor preferred term: assigning a centrally registered identifier
has curation status: IAO_0000120

associating information with a centrally registered identifier in its registry
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
example of usage: Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
alternative term: associating information with a CRID in the CRID registry
term editor: PERSON:Alan Ruttenberg
editor preferred term: associating information with a centrally registered identifier in its registry
has curation status: IAO_0000120

obsolete_establishing a CRID registry
type: Class
subclass of: ObsoleteClass
definition: a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
editor preferred term: obsolete_establishing a CRID registry
deprecated: true
editor note: MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
has obsolescence reason: IAO_0000103

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: centrally registered identifier
alternative term: CRID symbol
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
editor preferred term: centrally registered identifier symbol
has curation status: IAO_0000120

centrally registered identifier
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
alternative term: CRID
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
editor preferred term: centrally registered identifier
has curation status: IAO_0000120

centrally registered identifier registry
type: Class
subclass of: data set
alternative term: CRID registry
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
editor preferred term: centrally registered identifier registry
has curation status: IAO_0000120

looking up a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
subclass of: Restriction
  on property: has_specified_input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
example of usage: Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: looking up a CRID
editor preferred term: looking up a centrally registered identifier
has curation status: IAO_0000120

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
editor preferred term: time stamped measurement datum
has curation status: IAO_0000123

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: time stamped measurement datum
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
term editor: Alan Ruttenberg
alternative term: experimental time series
example of usage: pmid:20604925 - time-lapse live cell microscopy
editor preferred term: time sampled measurement data set
has curation status: IAO_0000120

written name
type: Class
subclass of: textual entity
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
definition: A textual entity that denotes a particular in reality.
term editor: PERSON: Bill Hogan
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: written name
has curation status: IAO_0000125

software method
type: Class
subclass of: software
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: software method
has curation status: IAO_0000123

software module
type: Class
subclass of: software
definition: A software module is software composed of a collection of software methods.
term editor: PERSON: Melanei Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: software module
has curation status: IAO_0000123

software library
type: Class
subclass of: software
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: software library
has curation status: IAO_0000123

software application
type: Class
subclass of: software
definition: A software application is software that can be directly executed by some processing unit.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: software application
has curation status: IAO_0000123

software script
type: Class
subclass of: software
definition: A software script is software whose instructions can be executed using a software interpreter.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: software script
has curation status: IAO_0000123

infection
type: Class
subclass of: material entity
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.
editor preferred term: infection
imported from: ido.owl

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

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

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

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

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
editor preferred term: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl

Ecdysozoa
type: Class
subclass of: Bilateria
editor preferred term: Ecdysozoa
imported from: ncbitaxon.owl

Pancrustacea
type: Class
subclass of: Ecdysozoa
editor preferred term: Pancrustacea
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: OBI_0100026
editor preferred term: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl

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

Eukaryota
type: Class
subclass of: OBI_0100026
editor preferred term: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
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 term: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred term: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred term: Opisthokonta
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred term: Bilateria
imported from: ncbitaxon.owl

Arabidopsis thaliana
type: Class
subclass of: Eukaryota
editor preferred term: Arabidopsis thaliana
alternative term: mouse-ear cress
alternative term: thale cress
alternative term: thale-cress
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 term: 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 term: ascomycetes
alternative term: sac fungi
imported from: ncbitaxon.owl

Schizosaccharomyces pombe
type: Class
subclass of: Ascomycota
editor preferred term: Schizosaccharomyces pombe
alternative term: fission yeast
imported from: ncbitaxon.owl

Saccharomyces cerevisiae
type: Class
subclass of: saccharomyceta
editor preferred term: Saccharomyces cerevisiae
alternative term: baker's yeast
alternative term: brewer's yeast
alternative term: lager beer yeast
alternative term: yeast
imported from: ncbitaxon.owl

Neurospora
type: Class
subclass of: saccharomyceta
editor preferred term: Neurospora
imported from: ncbitaxon.owl

Caenorhabditis elegans
type: Class
subclass of: Ecdysozoa
editor preferred term: Caenorhabditis elegans
alternative term: nematode
imported from: ncbitaxon.owl

Daphnia
type: Class
subclass of: Pancrustacea
editor preferred term: Daphnia
alternative term: common water fleas
imported from: ncbitaxon.owl

saccharomyceta
type: Class
subclass of: Ascomycota
editor preferred term: saccharomyceta
imported from: ncbitaxon.owl

Drosophila melanogaster
type: Class
subclass of: Pancrustacea
editor preferred term: Drosophila melanogaster
alternative term: fruit fly
imported from: ncbitaxon.owl

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
alternative term: Vertebrata
editor preferred term: Vertebrata <Metazoa>
alternative term: vertebrates
imported from: ncbitaxon.owl

Danio rerio
type: Class
subclass of: Euteleostomi
editor preferred term: Danio rerio
alternative term: leopard danio
alternative term: zebra danio
alternative term: zebra fish
alternative term: zebrafish
imported from: ncbitaxon.owl

Xenopus <genus>
type: Class
subclass of: Tetrapoda
alternative term: Xenopus
editor preferred term: Xenopus <genus>
imported from: ncbitaxon.owl

Gallus gallus
type: Class
subclass of: Amniota
editor preferred term: Gallus gallus
alternative term: bantam
alternative term: chicken
alternative term: chickens
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred term: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
imported from: ncbitaxon.owl

Rodentia
type: Class
subclass of: Euarchontoglires
editor preferred term: Rodentia
alternative term: rodents
imported from: ncbitaxon.owl

role of being consumer safety officer
type: Class
subclass of: role of regulator of consumables and medical devices
term editor: Person:Helen Parkinson
definition: the role of a human being that is realized by enforcing regulations to ensure consumer safety
example of usage: Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
term editor: Jennifer Fostel
definition source: OBI, CDISC
example of usage: Person charged with serving as CSO, FDA official who coordinates the review
editor preferred term: role of being consumer safety officer
has curation status: IAO_0000120

fluorescent reporter intensity
type: Class
subclass of: measurement datum
definition source: group:OBI
definition: A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
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.
editor preferred term: fluorescent reporter intensity
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

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 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.)
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
term editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
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.
definition source: branch derived
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
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)
editor preferred term: planned process
has curation status: IAO_0000122
imported from: Ontology for Biomedical Investigation

regulator role
type: Class
subclass of: regulatory role
alternative term: regulator
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
definition source: OBI
term editor: Person:Jennifer Fostel
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
editor preferred term: regulator role
has curation status: IAO_0000120

biological feature identification objective
type: Class
subclass of: objective specification
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
editor preferred term: biological feature identification objective
has curation status: IAO_0000123

regulation-assigned role
type: Class
subclass of: regulatory role
example of usage: Approval letter
term editor: Person: Jennifer Fostel
definition: Regulation-assigned role is a regulatory role defined by legislation or governmental orders
editor preferred term: regulation-assigned role
has curation status: IAO_0000123

regulatory role
type: Class
subclass of: role
term editor: GROUP: Role branch
definition source: OBI, CDISC
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
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.
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
editor preferred term: regulatory role
has curation status: IAO_0000120

material supplier role
type: Class
subclass of: service provider role
example of usage: Jackson Labs is an organization which provide mice as experimental material
editor note: Supplier role is a special kind of service, e.g. biobank
alternative term: material provider role
alternative term: supplier
term editor: PERSON:Jennifer Fostel
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor preferred term: material supplier role
has curation status: IAO_0000120

contract research organization role
type: Class
subclass of: worker role
alternative term: contract research organization
term editor: Person: Jennifer Fostel
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
editor preferred term: contract research organization role
has curation status: IAO_0000123

list-mode data file
type: Class
subclass of: information content entity
definition source: group:Flow Cytometry community
definition: A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
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.
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.
editor preferred term: list-mode data file
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

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
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned class labels
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.
editor preferred term: classified data set
has curation status: IAO_0000125

reference substance role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
alternative term: reference substance
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
definition source: OBI
term editor: Person:Jennifer Fostel
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.
editor preferred term: reference substance role
has curation status: IAO_0000120

cytological stain role
type: Class
subclass of: dye role
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
alternative term: cytological stain
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
term editor: Person:Jennifer Fostel
editor preferred term: cytological stain role
has curation status: IAO_0000120

centrifuge pellet role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: OBI_0302886
curator note: 9Mar09 after discussion with process branch changed definition to include use of centrifuge;
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
term editor: GROUP: Role branch
definition source: OBI
editor preferred term: centrifuge pellet role
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..
has curation status: IAO_0000125

clinical research coordinator role
type: Class
subclass of: worker role
alternative term: clinical research coordinator
term editor: Person:Jennifer Fostel
definition: a worker role comprised of handling the administrative duties of a trial or study.
editor preferred term: clinical research coordinator role
has curation status: IAO_0000123

supernatant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: OBI_0600014
term editor: GROUP: Role branch
definition source: OBI
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
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.
editor preferred term: supernatant role
has curation status: IAO_0000120

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
curator note: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
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
editor preferred term: chromatography column
definition source: http://en.wikipedia.org/wiki/Column_chromatography
has curation status: IAO_0000123

drug role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: molecular entity
alternative term: drug
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.
definition source: OBI, CDISC
term editor: Role Branch
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
editor preferred term: drug role
has curation status: IAO_0000120

pump valve switch
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
definition source: OBI
term editor: OBI Instrument branch
editor preferred term: pump valve switch
has curation status: IAO_0000123

xenotransplantation
type: Class
subclass of: transplantation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
definition: is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
editor preferred term: xenotransplantation
has curation status: IAO_0000125

physical document
type: Class
subclass of: processed material
definition source: GROUP: OBI
term editor: PERSON: Bjoern Peters
definition: A physical document is an object serving as a record of information by means of symbolic marks.
example of usage: a book is a physical document
editor preferred term: physical document
has curation status: IAO_0000120

waiting
type: Class
subclass of: OBI_0600009
curator note: BP: I have doubts about the utility of this.
definition source: OBI branch derived
term editor: PERSON:Alan Ruttenberg
curator note: We need a better handling/modeling of time (January 2008)
definition: not actively doing anything to a material for a duration of time.
editor preferred term: waiting
has curation status: IAO_0000125

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
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
editor preferred term: processed material
has curation status: IAO_0000122

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: environment control function
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
subclass of: Restriction
  on property: has function
  some values from: contain function
curator note: open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
term editor: Frank Gibson
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.
editor preferred term: chromatography device
alternative term: chromatography instrument
definition source: http://en.wikipedia.org/wiki/Chromatography
has curation status: IAO_0000120

mass spectrometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has_supplier
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: mass analyzer
  intersection of: Restriction
    on property: has part
    some values from: ion source
  intersection of: Restriction
    on property: has part
    some values from: ion detector
subclass of: Restriction
  on property: bearer of
  some values from: device setting
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
example of usage: LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry
editor preferred term: mass spectrometer
has curation status: IAO_0000122

obsolete_platform
type: Class
subclass of: ObsoleteClass
definition source: OBI Instrument branch
term editor: OBI Instrument branch
curator note: suggested for deprecation https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
deprecated: true
definition: A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
editor preferred term: obsolete_platform
curator note: rem1: We decided at the Philly workshop that consumables do not include reagents. FG: we could actully add a relation to platform which would be "has_part some instrument" DS: Sounds fine to me, with the restriction that I would assume a min. cardinality of 2 to be applicable for this crossproduct, so at least 2 instruments make it a platform... at least one is not enough AR:has_part is transitive, and transitive properties can't have cardinality constraints in OWL-DL. We can always put this particular constraint in the owl-full file. We need to make this a defined class when the class software is in the ontology
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

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: 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
subclass of: Restriction
  on property: has part
  some values from: chromatography device
definition source: OBI Instrument branch
term editor: OBI instrument branch
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.
editor preferred term: liquid chromatography mass spectrometry platform
has curation status: IAO_0000123

microarray platform
type: Class
subclass of: OBI_0002089
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
definition source: OBI Instrument branch
term editor: OBI Instrument branch
definition: A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
editor preferred term: microarray platform
has curation status: IAO_0000123

ratio of collected to emitted light
type: Class
subclass of: measurement datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 10%
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
editor preferred term: ratio of collected to emitted light
has curation status: IAO_0000120

software optimization objective
type: Class
subclass of: software testing objective
term editor: Jennifer Fostel
definition: Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
editor preferred term: software optimization objective
has curation status: IAO_0000123

notified body role
type: Class
subclass of: role of regulator of consumables and medical devices
alternative term: notified body
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.
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
definition source: OBI, CDISC
term editor: Person: Jennifer Fostel
example of usage: The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
editor preferred term: notified body role
has curation status: IAO_0000120

allotransplantation
type: Class
subclass of: transplantation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: allotransplantation
definition: is the transplantation of organs between members of the same species.
has curation status: IAO_0000125

gamma counter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
example of usage: A Geiger counter
definition: A processed material which measures gamma radiation
term editor: Frank Gibson
editor preferred term: gamma counter
definition source: http://en.wikipedia.org/wiki/Gamma_counter
has curation status: IAO_0000122

trial monitor role
type: Class
subclass of: responsible party role
alternative term: 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.
term editor: Person:Jennifer Fostel
definition: a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
editor preferred term: trial monitor role
has curation status: IAO_0000123

positive reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: assay
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
alternative term: positive reference substance
example of usage: MMS mutagen
term editor: Person: Jennifer Fostel
editor preferred term: positive reference substance role
has curation status: IAO_0000123

polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
type: Class
subclass of: molecular entity
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.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia before possible import from CHEBI
editor preferred term: polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
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
has curation status: IAO_0000123

investigation
type: Class
subclass of: planned process
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: documenting
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
curator note: Could add specific objective specification
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
ISA alternative term: study
term editor: Bjoern Peters
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
definition source: OBI branch derived
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred term: investigation
has curation status: IAO_0000122
imported from: Ontology for Biomedical Investigation

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
term editor: GROUP: Role Branch
definition source: OBI
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)
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.
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 preferred term: evaluant role
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
has curation status: IAO_0000122

reporting party role
type: Class
subclass of: investigation agent role
editor note: MO:submitter mapped to this term. So, alternative term 'submitter' was added.
example of usage: Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
alternative term: reporting party
alternative term: submitter
term editor: Jennifer Fostel
definition source: OBI
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
definition: a study personnel role played by a party who reports the outcome of a study component
editor preferred term: reporting party role
has curation status: IAO_0000120

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: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
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: realizes
  some values from: evaluant role
disjoint with: planning
disjoint with: OBI_0200000
disjoint with: OBI_0600013
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
IEDB alternative term: any method
ISA alternative term: study assay
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.
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: assay
alternative term: measuring
alternative term: scientific observation
has curation status: IAO_0000122

quantitative confidence value
type: Class
subclass of: data item
definition source: group:OBI
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
term editor: person:Chris Stoeckert
editor preferred term: quantitative confidence value
has curation status: IAO_0000125

sample preparation for assay
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: sample preparation for assay
alternative term: study
has curation status: IAO_0000125

diagnosis textual entity
type: Class
subclass of: textual entity
term editor: Jennifer Fostel
definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
editor preferred term: diagnosis textual entity
has curation status: IAO_0000123

unplanned occurrence effecting an investigation
type: Class
subclass of: process
definition source: OBI
term editor: PERSON: Bjoern Peters
example of usage: Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
definition: a process which is external in origin to the investigation that has an impact on the outcome.
editor preferred term: unplanned occurrence effecting an investigation
has curation status: IAO_0000120

eMedical record
type: Class
subclass of: information content entity
definition source: article-without-pmid-or-doi:CDISCglossary
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.
editor preferred term: eMedical record
term editor: person:Jennifer Fostel
has curation status: IAO_0000125

culture medium
type: Class
subclass of: processed material
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.
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
definition source: OBI
term editor: Person: Jennifer Fostel, Jie Zheng
editor preferred term: culture medium
has curation status: IAO_0000122

electronic case report tabulation
type: Class
subclass of: information content entity
definition source: CDISC glossary
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.
editor preferred term: electronic case report tabulation
term editor: person:Jennifer Fostel
has curation status: IAO_0000120

polystyrene tube
type: Class
subclass of: test tube
term editor: PERSON: Chris Stoeckert
definition source: PERSON: Chris Stoeckert
example of usage: Polystyrene tubes can be used to contain tissue culture cells during centrifgation
definition: a polystyrene tube is a test tube made of polystyrene
editor preferred term: polystyrene tube
has curation status: IAO_0000122

reagent role
type: Class
subclass of: role
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.
definition source: PERSON:Matthew Brush
alternative term: reagent
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…
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.
example of usage: Buffer, dye, a catalyst, a solvating agent.
term editor: PERSON:Matthew Brush
editor preferred term: reagent role
has curation status: IAO_0000120

role of regulator of chemical manufacturer
type: Class
subclass of: regulator role
alternative term: regulator of chemical manufacture
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
definition source: OBI
term editor: Person: Jennifer Fostel
definition: a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
editor preferred term: role of regulator of chemical manufacturer
has curation status: IAO_0000120

detector reagent role
type: Class
subclass of: role
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
definition: a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
editor preferred term: detector reagent role
has curation status: IAO_0000123

role of certified IRB professional
type: Class
subclass of: regulation-assigned role
term editor: Person:Helen Parkinson
definition source: WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
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
alternative term: certified IRB professional
example of usage: CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
term editor: Person:Jennifer Fostel
editor preferred term: role of certified IRB professional
has curation status: IAO_0000120

patient role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
alternative term: patient
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
term editor: GROUP:Role Branch
definition source: OBI, CDISC
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
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 preferred term: patient role
has curation status: IAO_0000120

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_input
  all values from: material entity
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
disjoint with: OBI_0600010
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
definition: A planned process which results in physical changes in a specified input material
definition source: OBI branch derived
term editor: PERSON: Bjoern Peters
editor preferred term: material processing
alternative term: material transformation
has curation status: IAO_0000122

protocol testing objective
type: Class
subclass of: methodology testing objective
term editor: Jennifer Fostel
definition: Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
editor preferred term: protocol testing objective
has curation status: IAO_0000123

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
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.
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.
definition source: OBI
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.
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
term editor: GROUP: Role Branch
editor preferred term: participant under investigation role
has curation status: IAO_0000122

obsolete_role of being first subject treated
type: Class
subclass of: ObsoleteClass
definition source: OBI
deprecated: true
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
example of usage: Rat 1A; first enrolled patient to receive treatment
term editor: Role Branch
editor note: first subject treated. First subject who receives the test article or placebo in a clinical trial.
editor preferred term: obsolete_role of being first subject treated
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

measured expression level
type: Class
subclass of: measurement datum
definition source: OBI Data Transformation branch
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.
example of usage: Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
editor preferred term: measured expression level
term editor: person:Chris Stoeckert
has curation status: IAO_0000120

responsible party role
type: Class
subclass of: investigation agent role
alternative term: responsible party
definition source: OBI
term editor: Person: Jennifer Fostel
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
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
editor preferred term: responsible party role
has curation status: IAO_0000120

principal investigator role
type: Class
subclass of: responsible party role
alternative term: 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)
term editor: Person: Jennifer Fostel
definition: a responsible party role played by a person responsible for the overall conduct of a study
editor preferred term: principal investigator role
has curation status: IAO_0000123

transplantation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
definition: a protocol application to replace an organ or tissue of an organism
editor preferred term: transplantation
has curation status: IAO_0000125

biological vector role
type: Class
subclass of: ObsoleteClass
curator note: 6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
editor note: Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
term editor: GROUP: Role Branch
definition source: OBI and Wikipedia
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.
editor note: false
deprecated: true
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
editor preferred term: biological vector role
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

pH indicator dye role
type: Class
subclass of: dye role
term editor: Person:Helen Parkinson
example of usage: bromophenol blue has a pH indicator dye role
alternative term: pH indicator dye
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
editor preferred term: pH indicator dye role
example of usage: phenol red in RPMI; pH=4 indicator dye (also carries reference role)
has curation status: IAO_0000120

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
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.
term editor: GROUP: Role Branch
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.
definition source: OBI
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.
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
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.
editor preferred term: specimen role
has curation status: IAO_0000122

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
term editor: Jennifer Fostel
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.
editor preferred term: sequence feature identification objective
has curation status: IAO_0000123

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
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.
definition source: OBI branch derived
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.
term editor: Philppe Rocca-Serra
editor preferred term: intervention design
has curation status: IAO_0000125

worker role
type: Class
subclass of: investigation agent role
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
alternative term: worker
definition source: OBI
term editor: Person:Jennifer Fostel
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
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 preferred term: worker role
has curation status: IAO_0000120

Bernoulli trial
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: Bernoulli trial
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
definition: is an assay where the output data is a datum with one of two values denoted success and failure.
has curation status: IAO_0000125

gene list
type: Class
subclass of: data set
definition source: group:OBI
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.
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.
editor preferred term: gene list
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.
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

number of particles in subset
type: Class
subclass of: measurement datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 500, 200, 0
definition: A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
editor preferred term: number of particles in subset
term editor: person:Kevin Clancy
has curation status: IAO_0000120

number of lost events electronic
type: Class
subclass of: measurement datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 74, 0, 14 events lost due to data acquisition electronic coincidence.
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.
editor preferred term: number of lost events electronic
term editor: person:Kevin Clancy
has curation status: IAO_0000120

calibration substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: calibration
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
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

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
term editor: Jennifer Fostel
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.
editor preferred term: molecular feature identification objective
has curation status: IAO_0000123

hardware testing objective
type: Class
subclass of: methodology testing objective
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
editor preferred term: hardware testing objective
has curation status: IAO_0000123

incubator
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: environment control function
term editor: Frank Gibson
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
definition: a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
definition source: http://www.medterms.com/script/main/art.asp
editor preferred term: incubator
has curation status: IAO_0000120

obsolete_label role
type: Class
subclass of: ObsoleteClass
definition source: OBI
alternative term: label
deprecated: true
term replaced by: http://purl.obolibrary.org/obo/REO_0000171
editor note: MHB (9-26-12): consider deprecation of this class and replacement with REO:'molecular label role'
definition: Label role is a role which inheres in a material entity and which is realized in a detection of label assay
editor note: Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion
term editor: Role Branch
editor note: need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity
editor preferred term: obsolete_label role
editor note: we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&aid=1866458&group_id=177891&atid=886178
has obsolescence reason: IAO_0000228
has curation status: IAO_0000428

baseline participant role
type: Class
subclass of: reference subject role
definition: a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
alternative term: baseline participant
term editor: Person: Jennifer Fostel
example of usage: Subject at time = 0; subject before a stress test.
editor preferred term: baseline participant role
has curation status: IAO_0000123

role of independent data monitoring committee
type: Class
subclass of: trial monitor role
alternative term: independent data monitoring committee
term editor: Person: Jennifer Fostel
definition: a trial monitor role charged recommending whether to continue, modify, or end the trial
editor preferred term: role of independent data monitoring committee
has curation status: IAO_0000120

pathologist role
type: Class
subclass of: worker role
alternative term: Pathologist
term editor: Person:Jennifer Fostel
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
editor preferred term: pathologist role
has curation status: IAO_0000123

supernatant collection system harvesting frame
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
term editor: Daniel Schober
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.
definition source: google
editor preferred term: supernatant collection system harvesting frame
has curation status: IAO_0000120

filter paper
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
term editor: Frank Gibson
definition: a device manufacture with the intent to provide a porous unsized paper used for filtering.
editor preferred term: filter paper
definition source: sep:00107
has curation status: IAO_0000120

cell co-culturing
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
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
definition: A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
example of usage: Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: cell co-culturing
has curation status: IAO_0000125

role of Institutional Review Board
type: Class
subclass of: regulator role
example of usage: Animal protocol review board
alternative term: Internal Review Board
term editor: Person:Helen Parkinson
definition: the role of a organization that is realized by members reviewing study designs for their agreement with regulations
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
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.
definition source: OBI, CDISC
term editor: Person:Jennifer Fostel
editor preferred term: role of Institutional Review Board
has curation status: IAO_0000120

eSource document
type: Class
subclass of: information content entity
definition source: article-without-pmid-or-doi:CDISCglossary
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
editor preferred term: eSource document
term editor: person:Jennifer Fostel
has curation status: IAO_0000125

crossover population role
type: Class
subclass of: reference subject role
definition: a role realized when a participant serves as reference to itself
alternative term: crossover population
term editor: Person: Jennifer Fostel
editor preferred term: crossover population role
has curation status: IAO_0000123

complete nutrient role
type: Class
subclass of: nutrient role
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.
alternative term: complete nutrient
term editor: Person: Jennifer Fostel
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
editor preferred term: complete nutrient role
has curation status: IAO_0000123

radiolabel role
type: Class
subclass of: REO_0000171
subclass of: Restriction
  on property: realized in
  all values from: radioactivity detection
term editor: Jennifer Fostel
definition: a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection
alternative term: radiolabel
editor preferred term: radiolabel role
has curation status: IAO_0000120

cDNA library
type: Class
subclass of: recombinant vector
subclass of: Restriction
  on property: has grain
  some values from: recombinant vector
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600064
definition source: GROUP: PSI
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
example of usage: PMID:6110205. collection of cDNA derived from mouse splenocytes.
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
editor preferred term: cDNA library
has curation status: IAO_0000123

electronic case report form
type: Class
subclass of: information content entity
definition source: CDISC glossary
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.
editor preferred term: electronic case report form
term editor: person:Jennifer Fostel
has curation status: IAO_0000120

placebo role
type: Class
subclass of: negative reference substance role
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
alternative term: 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.
term editor: Person:Jennifer Fostel
example of usage: Pill consisting of inert materials
editor preferred term: placebo role
has curation status: IAO_0000120

autotransplantation
type: Class
subclass of: transplantation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: autotransplantation
definition: is the transplantation of tissue from one part of \nthe body to another in the same individual. )
has curation status: IAO_0000125

parameter threshold
type: Class
subclass of: measurement datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 0.01, 0.03
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
editor preferred term: parameter threshold
term editor: person:Kevin Clancy
has curation status: IAO_0000120

study group role
type: Class
subclass of: role
example of usage: The group of randomized participants that are assigned to a treatment arm of the trial
alternative term: study group population
term editor: Jennifer Fostel
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
editor preferred term: study group role
has curation status: IAO_0000123

p-value
type: Class
subclass of: quantitative confidence value
editor note: May be outside the scope of OBI long term, is needed so is retained
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).
definition source: WEB: http://en.wikipedia.org/wiki/P-value
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.
term editor: PERSON:Chris Stoeckert
editor preferred term: p-value
has curation status: IAO_0000121

population
type: Class
subclass of: material entity
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
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.
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
definition source: adapted from Oxford English Dictionnary
editor preferred term: population
curator note: rem1: collection somehow always involve a selection process
has curation status: IAO_0000125

nuclear magnetic resonance 3D structure determination assay
type: Class
equivalent class: Class
  intersection of: OBI_0600045
  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_0600045
definition: A 3D structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample.
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).
definition source: IEDB
term editor: PlanAndPlannedProcess Branch, IEDB
editor preferred term: nuclear magnetic resonance 3D structure determination assay
has curation status: IAO_0000120

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: image
definition: An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: imaging assay
has curation status: IAO_0000125

protocol optimization objective
type: Class
subclass of: protocol testing objective
term editor: Jennifer Fostel
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.
editor preferred term: protocol optimization objective
has curation status: IAO_0000123

role of pathology review board
type: Class
subclass of: worker role
alternative term: pathology review board
term editor: Person: Jennifer Fostel
definition: a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
editor preferred term: role of pathology review board
has curation status: IAO_0000123

microtiter plate
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
example of usage: A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
definition: A microtiter_plate is a flat plate with multiple wells used as small test tubes.
term editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Microtiter_plate
alternative term: microplate
editor preferred term: microtiter plate
has curation status: IAO_0000122

role of impartial witness
type: Class
subclass of: regulation-assigned role
term editor: Person: Helen Parkinson
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
alternative term: 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
term editor: Person: Jennifer Fostel
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
editor preferred term: role of impartial witness
has curation status: IAO_0000123

chromatin immunoprecipitation
type: Class
subclass of: immunoprecipitation
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 term: ChIP
definition source: OBI
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.
editor preferred term: chromatin immunoprecipitation
has curation status: IAO_0000120

biological replicate role
type: Class
subclass of: reference subject role
definition: a reference participant role realized by equivalent treatment of participants
alternative term: biological replicate
example of usage: A member of a dose-time group; a patient in a given arm of a trial
definition source: OBI
term editor: Person:Jennifer Fostel
editor preferred term: biological replicate role
has curation status: IAO_0000120

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: bearer of
        some values from: PATO_0001741
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: Restriction
        on property: realizes
        some values from: PATO_0001741
subclass of: assay
definition: An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
definition source: IEDB
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.
term editor: PlanAndPlannedProcess Branch, IEDB
editor preferred term: radioactivity detection
has curation status: IAO_0000120

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: Restriction
      on property: bearer of
      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
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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 preferred term: investigation agent role
alternative term: investigator
ISA alternative term: study person role
term editor: GROUP: Role Branch
definition source: OBI
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)
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)
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.
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

nutrient role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
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.
alternative term: nutrient
term editor: GROUP: Role branch
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.
definition source: Wikipedia, feb 29, 2008
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.
editor preferred term: nutrient role
has curation status: IAO_0000120

obsolete_dropout role
type: Class
subclass of: ObsoleteClass
definition source: OBI
editor note: Will be modelled as defined material, ouput of some 'dropout or withdrawal process' instead of role
deprecated: true
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.
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)
term editor: Role Branch
editor preferred term: obsolete_dropout role
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

health care provider role
type: Class
subclass of: worker role
alternative term: health care provider
term editor: Person:Jennifer Fostel
definition: a worker role of providing medical care either within or outside the study timeline
editor preferred term: health care provider role
has curation status: IAO_0000120

methodology testing objective
type: Class
subclass of: objective specification
term editor: Jennifer Fostel
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.
editor preferred term: methodology testing objective
has curation status: IAO_0000123

analytical cytology data file
type: Class
subclass of: information content entity
definition source: group:Flow Cytometry community
definition: A digital entity intended to capture data in analytical cytology domain.
example of usage: FCS file, ACS file, foo.fcs, foo.asc
editor preferred term: analytical cytology data file
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

proxy respondent role
type: Class
subclass of: worker role
alternative term: proxy respondent
term editor: Jennifer Fostel
definition: Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
editor preferred term: proxy respondent role
has curation status: IAO_0000120

fluorescence compensation matrix
type: Class
subclass of: information content entity
definition source: group:Flow Cytometry community
example of usage: ((1.053096, -0.22476), (-0.24877, 1.053096))
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.
editor preferred term: fluorescence compensation matrix
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

negative reference substance role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: assay
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
alternative term: negative reference substance
term editor: Person: Jennifer Fostel
example of usage: Saline solution
editor preferred term: negative reference substance role
has curation status: IAO_0000123

role of legally acceptable representative
type: Class
subclass of: regulation-assigned role
term editor: Person:Helen Parkinson
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.
alternative term: legally acceptable representative
definition source: OBI, CDISC
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
term editor: Person: Jennifer Fostel
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]
editor preferred term: role of legally acceptable representative
has curation status: IAO_0000120

investigation results report
type: Class
subclass of: report
definition source: group:OBI
definition: An investigation report is a report on the results of an investigation.
editor preferred term: investigation results report
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

cellular feature identification objective
type: Class
subclass of: biological feature identification objective
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
editor preferred term: cellular feature identification objective
has curation status: IAO_0000123

reference subject role
type: Class
subclass of: participant under investigation role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: OBI_0100026
    union of: OBI_0100051
alternative term: reference participant
term editor: Jennifer Fostel
definition source: OBI
example of usage: Saline treated rat; one of three identically-treated subjects
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
editor preferred term: reference subject role
has curation status: IAO_0000120

vital dye role
type: Class
subclass of: dye role
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
definition: A dye role that is realized when used to detect live cells in an experiment
term editor: Person: Helen Parkinson
example of usage: typtan blue has a vital dye
alternative term: vital dye
term editor: Person: Jennifer Fostel
editor preferred term: vital dye role
has curation status: IAO_0000120

obsolete_blinded medication role
type: Class
subclass of: ObsoleteClass
example of usage: 115 patients received ipilimumab and blinded medication
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: Person:Helen Parkinson
editor note: Will be modelled using a blinding process and specified output blinded medication instead
deprecated: true
example of usage: Inert pill shaped like aspirin tablet
term editor: Jennifer Fostel
editor preferred term: obsolete_blinded medication role
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

sub-investigator role
type: Class
subclass of: worker role
alternative term: 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
term editor: Person: Jennifer Fostel
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
editor preferred term: sub-investigator role
has curation status: IAO_0000123

data encoding
type: Class
subclass of: documenting
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
curator note: We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
definition: a documenting process to encode an information entity into a digital document
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

enzymatic 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: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: enzyme
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
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
editor preferred term: enzymatic cleavage
definition: enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
has curation status: IAO_0000125

hardware optimization objective
type: Class
subclass of: hardware testing objective
definition: Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
term editor: Jennifer Fostel
editor preferred term: hardware optimization objective
has curation status: IAO_0000123

obsolete_defined_material
type: Class
subclass of: ObsoleteClass
definition source: OBI Biomaterial derived
term editor: Susanna Sansone
editor note: false
deprecated: true
definition: Place holder class, Utility class to gather the defined classes
editor preferred term: obsolete_defined_material
has curation status: IAO_0000121
has obsolescence reason: IAO_0000226

trial statistician role
type: Class
subclass of: worker role
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0500001
  intersection of: Restriction
    on property: realized in
    all values from: investigation
alternative term: 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]
term editor: Person:Jennifer Fostel
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.
editor preferred term: trial statistician role
has curation status: IAO_0000123

standard error
type: Class
subclass of: quantitative confidence value
definition source: group:OBI
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
curator note: see P-Value
editor preferred term: standard error
has curation status: IAO_0000125

antigen role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: immune response
curator note: 9Mar09 waiting for discussion with immunology terms
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
definition source: OBI
definition: Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
term editor: Role Branch
editor preferred term: antigen role
has curation status: IAO_0000123

software testing objective
type: Class
subclass of: methodology testing objective
term editor: Jennifer Fostel
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.
editor preferred term: software testing objective
has curation status: IAO_0000123

sponsor role
type: Class
subclass of: responsible party role
alternative term: 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
term editor: Person: Jennifer Fostel
definition: a responsible party role involved with any of the following activities: initiating, managing and funding a study
editor preferred term: sponsor role
has curation status: IAO_0000120

organization
type: Class
subclass of: material entity
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
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.
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.
editor preferred term: organization
has curation status: IAO_0000122

feed role
type: Class
subclass of: complete nutrient role
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.
alternative term: feed
definition source: OBI
term editor: Person: Jennifer Fostel
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
editor preferred term: feed role
has curation status: IAO_0000120

technical replicate role
type: Class
subclass of: reference subject role
alternative term: technical replicate
definition: technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
example of usage: Aliquots of a tissue subjected to parallel assays
term editor: Person: Jennifer Fostel
editor preferred term: technical replicate role
has curation status: IAO_0000123

dye role
type: Class
subclass of: REO_0000171
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.
definition source: A substance used to color materials www.answers.com/topic/dye 19feb09
alternative term: dye
term editor: Jennifer Fostel
editor preferred term: dye role
has curation status: IAO_0000120

cluster
type: Class
subclass of: data set
definition source: group:OBI
definition: A data set which is a subset of data that are a similar to each other in some way.
example of usage: Cluster of the lymphocytes population.
editor preferred term: cluster
term editor: person:Allyson
term editor: person:Chris Stoeckert
has curation status: IAO_0000125

cohort role
type: Class
subclass of: biological replicate role
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.
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
term editor: Jennifer Fostel
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.
editor preferred term: cohort role
has curation status: IAO_0000123

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
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.
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
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

DNA extraction
type: Class
subclass of: OBI_0666667
subclass of: Restriction
  on property: has_specified_output
  some values from: deoxyribonucleic acid
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
editor preferred term: DNA extraction
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
has curation status: IAO_0000123

plan
type: Class
subclass of: realizable entity
example of usage: The plan of researcher X to perform an experiment according to a protocol.
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.
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
term editor: AR, BP, JM, MC, PRS
definition source: branch derived
editor preferred term: plan
has curation status: IAO_0000125

obsolete_sample population
type: Class
subclass of: ObsoleteClass
editor note: 03/21/2010: BP, obsoleting this term, as it is duplicated by 'material sample'. Use that instead term instead, which now also has 'sample population' as an alternative label.
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Philippe Rocca-Serra
deprecated: true
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.
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
editor preferred term: obsolete_sample population
alternative term: recruited population
has curation status: IAO_0000120
has obsolescence reason: IAO_0000227

organism feature identification objective
type: Class
subclass of: biological feature identification objective
term editor: Jennifer Fostel
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.
editor preferred term: organism feature identification objective
has curation status: IAO_0000123

number of lost events computer
type: Class
subclass of: measurement datum
definition source: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
example of usage: 0, 125, 787 events lost due to computer busy.
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
editor preferred term: number of lost events computer
term editor: person:Kevin Clancy
has curation status: IAO_0000120

protocol
type: Class
subclass of: plan specification
ISA alternative term: study protocol
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.
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
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.
term editor: PlanAndPlannedProcess Branch
editor preferred term: protocol
has curation status: IAO_0000122

role of regulator of consumables and medical devices
type: Class
subclass of: regulator role
alternative term: drug regulatoy authority
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
definition source: OBI, CDISC
term editor: Person: Jennifer Fostel
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
editor preferred term: role of regulator of consumables and medical devices
has curation status: IAO_0000120

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: target of material addition role
subclass of: Restriction
  on property: realizes
  some values from: material to be added 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
term editor: BP
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
definition source: branch derived
editor preferred term: adding a material entity into a target
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'.
has curation status: IAO_0000122

analyte role
type: Class
subclass of: role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
subclass of: Restriction
  on property: realized in
  all values from: analyte assay
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
term editor: GROUP: Role Branch
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
definition source: OBI
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.
definition: A 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 preferred term: analyte role
has curation status: IAO_0000122

disease stage
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: part of
  some values from: OGMS_0000063
term editor: PERSON: Bjoern peters
example of usage: Stage II breast cancer, The timepoint of recovery from a disease
definition: a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
editor preferred term: disease stage
has curation status: IAO_0000123

intraperitoneal 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: inheres in
        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_0002358
subclass of: injection
subclass of: intraperitoneal administration
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: BP
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
editor preferred term: intraperitoneal injection
has curation status: IAO_0000123

precipitate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600034
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Philippe Rocca-Serra
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
definition: a precipitate is a material entity which is output of a precipitation process
editor preferred term: precipitate
alternative term: precipited material
has curation status: IAO_0000120

protein-protein interaction detection
type: Class
subclass of: assay
editor note: 20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays.
definition: An assay with the objective to determine interactions between proteins, such as protein-protein binding.
editor preferred term: protein-protein interaction detection
has curation status: IAO_0000123

transcription factor binding site assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection 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: transcription factor binding site
subclass of: binding assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: sequence-specific DNA binding
definition source: OBI
term editor: Philippe Rocca-Serra
editor note: JZ: fixed inconsistency issue and relabel the term see tracker: https://sourceforge.net/p/obi/obi-terms/767/
definition: An assay with objective to find DNA region specifically recognized by proteins that function as transcription factors
editor note: JZ: add equivalent axiom for classification add alternative term 'TF binding' which was used in BCBC database
alternative term: TF binding
example of usage: Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031
editor preferred term: transcription factor binding site assay
has curation status: IAO_0000120

obsolete_enrollment
type: Class
subclass of: ObsoleteClass
editor note: merged with 'enrollment of human subjects
deprecated: true
term editor: Bjoern Peters
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
definition source: IEDB
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
editor preferred term: obsolete_enrollment
has curation status: IAO_0000125
has obsolescence reason: IAO_0000227

adverse event trigger
type: Class
subclass of: conditional specification
definition source: OBI branch derived
term editor: PERSON:Alan Ruttenberg
editor preferred term: adverse event trigger
definition: revisit?
has curation status: IAO_0000125

eluate
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302905
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
definition source: OBI Bionaterial
term editor: PERSON: Philippe Rocca-Serra
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
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 preferred term: eluate
alternative term: eluted material
editor note: need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
has curation status: IAO_0000120

material to be added role
type: Class
subclass of: role
curator note: 9 March 09 from discussion with PA branch
definition source: OBI
term editor: Role Branch
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
editor preferred term: material to be added role
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
has curation status: IAO_0000120

obsolete_peritoneum
type: Class
subclass of: ObsoleteClass
deprecated: true
editor note: BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection
definition: is the serous membrane that forms the lining of the abdominal cavity
editor preferred term: obsolete_peritoneum
has curation status: IAO_0000002
has obsolescence reason: IAO_0000228

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
definition source: Bjoern Peters
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.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
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
editor preferred term: drawing a conclusion based on data
has curation status: IAO_0000122

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 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
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.
definition: a process of creating or modifying a plan specification
editor preferred term: planning
has curation status: IAO_0000122

obsolete_documenting
type: Class
subclass of: ObsoleteClass
editor note: 6/11/9: Edited at workshop. Should go into IAO. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
term replaced by: IAO_0000572
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
deprecated: true
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
editor preferred term: obsolete_documenting
has curation status: IAO_0000125
has obsolescence reason: IAO_0000228

histological sample preparation
type: Class
subclass of: material processing
subclass of: specimen collection process
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400168
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100066
definition source: OBI branch derived
term editor: PERSON:Bjoern Peters
editor preferred term: histological sample preparation
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
has curation status: IAO_0000125

inductive reasoning
type: Class
subclass of: drawing a conclusion based on data
term editor: Bjoern Peters
definition source: wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
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.
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.
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 preferred term: inductive reasoning
has curation status: IAO_0000428

mass analyzer
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: material separation function
term editor: Frank Gibson
term editor: PERSON: Daniel Schober
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer
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.
example of usage: The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
editor preferred term: mass analyzer
has curation status: IAO_0000120

hypothesis driven investigation
type: Class
subclass of: investigation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: hypothesis driven investigation
definition: is an investigation with the goal to test one or more hypothesis
has curation status: IAO_0000125

hypothesis generating investigation
type: Class
subclass of: investigation
definition source: OBI branch derived
term editor: PlanAndPlannedProcess Branch
editor preferred term: hypothesis generating investigation
definition: is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
has curation status: IAO_0000125

ion source
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: ionization function
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
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))).
example of usage: The ion source of a Voyager-DE??? STR Biospectrometry Workstation
editor preferred term: ion source
has curation status: IAO_0000122

ion detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
term editor: Frank Gibson
definition source: http://en.wikipedia.org/wiki/Mass_spectrometry#Detector
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.
example of usage: The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
editor preferred term: ion detector
has curation status: IAO_0000122

metabolite profiling
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100051
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition source: OBI
term editor: Philippe Rocca-Serra
alternative term: metabolite 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
editor preferred term: metabolite profiling
definition: metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
has curation status: IAO_0000120

light emission function
type: Class
subclass of: excitation function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
editor preferred term: light emission function
has curation status: IAO_0000122

record function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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
editor preferred term: record function
has curation status: IAO_0000122

magnify function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: magnify function
has curation status: IAO_0000122

contain function
type: Class
subclass of: function
example of usage: A syringe, a beaker
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A contain function is a function to constrain a material entities location in space
editor preferred term: contain function
has curation status: IAO_0000122

heat function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A heat function is a function that increases the internal kinetic energy of a material
editor preferred term: heat function
has curation status: IAO_0000122

material separation function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: material separation function
has curation status: IAO_0000122

ionize process
type: Class
subclass of: material processing
subclass of: Restriction
  on property: realizes
  some values from: ionization function
subclass of: Restriction
  on property: has participant
  some values from: continuant
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor note: 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
example of usage: Electrospray ionization in mass spectrometry
term editor: Person:Bjoern Peters
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 preferred term: ionize process
has curation status: IAO_0000123

excitation function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: excitation function
has curation status: IAO_0000122

freeze function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: freeze function
has curation status: IAO_0000122

synthesizing function
type: Class
subclass of: function
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
editor preferred term: synthesizing function
has curation status: IAO_0000122

perturb function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
definition source: http://en.wikipedia.org/wiki/Perturbation_biology
editor preferred term: perturb function
has curation status: IAO_0000122

filter function
type: Class
subclass of: material separation function
term editor: Frank Gibson
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
editor preferred term: filter function
has curation status: IAO_0000122

mechanical function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
definition source: http://en.wikipedia.org/wiki/Mechanical_work
editor preferred term: mechanical function
has curation status: IAO_0000122

gas filter function
type: Class
subclass of: filter function
term editor: Frank Gibson
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
editor preferred term: gas filter function
has curation status: IAO_0000122

liquid filter function
type: Class
subclass of: filter function
term editor: Frank Gibson
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
editor preferred term: liquid filter function
has curation status: IAO_0000122

transfer function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A transfer function is a function to displace a material from one location to another.
editor preferred term: transfer function
has curation status: IAO_0000122

electricity supply function
type: Class
subclass of: energy supply function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: the function of supplying current during a neuroscience experiment.
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.
editor preferred term: electricity supply function
alternative term: power supply
has curation status: IAO_0000122

ionization function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: The ion source in amass spectrometer
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.
definition source: http://en.wikipedia.org/wiki/Ionization
editor preferred term: ionization function
has curation status: IAO_0000122

cool function
type: Class
subclass of: function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: cool function
has curation status: IAO_0000122

connection function
type: Class
subclass of: function
example of usage: An electricity cable
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: connection function
has curation status: IAO_0000122

isoelectric focusing device
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: environment control function
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: bearer of
  some values from: device setting
subclass of: Restriction
  on property: has function
  some values from: transfer function
term editor: Frank Gibson
definition source: sep:00097
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.
editor preferred term: isoelectric focusing device
alternative term: isoelectric focusing unit
has curation status: IAO_0000120

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
term editor: Frank Gibson
definition source: sep:00098
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
editor preferred term: thermostatic circulator
has curation status: IAO_0000120

energy supply function
type: Class
subclass of: function
term editor: Frank Gibson
definition: An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
editor preferred term: energy supply function
has curation status: IAO_0000122

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
term editor: Frank Gibson
definition: An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
alternative term: data processor function
editor preferred term: information processor function
has curation status: IAO_0000122

signal conversion function
type: Class
subclass of: information processor function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
alternative term: transduction function
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.
editor preferred term: signal conversion function
has curation status: IAO_0000122

blot module
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
term editor: Frank Gibson
definition source: sep:00092
definition: A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
editor preferred term: blot module
has curation status: IAO_0000123

signal amplification function
type: Class
subclass of: signal conversion function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: signal amplification function
has curation status: IAO_0000122

image acquisition function
type: Class
subclass of: measure function
subclass of: Restriction
  on property: realized in
  all values from: image creation
subclass of: Restriction
  on property: inheres in
  some values from: image creation device
term editor: Frank Gibson
definition: An image acquisition function is a function to acquire an image of a material
editor preferred term: image acquisition function
has curation status: IAO_0000122

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
term editor: Frank Gibson
definition source: sep:00096
definition: An image creation device is a device which captures a digitized image of an object
alternative term: image acquisition device
editor preferred term: image creation device
has curation status: IAO_0000123

solid support function
type: Class
subclass of: function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
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
editor preferred term: solid support function
has curation status: IAO_0000122

display function
type: Class
subclass of: information processor function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
definition: A display function is a function to present information by translating that information through some lookup process into visual form.
editor preferred term: display function
has curation status: IAO_0000122

environment control function
type: Class
subclass of: function
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: environment control function
has curation status: IAO_0000122

sort function
type: Class
subclass of: material separation function
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
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.
editor preferred term: sort function
has curation status: IAO_0000122

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
term editor: Frank Gibson
definition source: sep:00094
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
editor preferred term: gel dryer
has curation status: IAO_0000120

primer role
type: Class
subclass of: complementary nucleotide probe role
subclass of: Restriction
  on property: realized in
  all values from: polymerase chain reaction
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
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.
editor preferred term: primer role
has curation status: IAO_0000123

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
definition source: GROUP: OBI BIomaterial Branch
term editor: GROUP: OBI BIomaterial Branch
example of usage: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
editor preferred term: PCR product
editor note: We are using PCR and not the written out words, as this is the most common used.
definition: is double stranded DNA that is the specified output of a polymerase chain reaction
has curation status: IAO_0000122

viral RNA extraction
type: Class
subclass of: OBI_0666666
subclass of: Restriction
  on property: has_specified_input
  some values from: Viruses
term editor: Person:Bjoern Peters
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
definition: The extraction of RNA from an input material that specifically isolates viral RNA
editor preferred term: viral RNA extraction
has curation status: IAO_0000123

nucleic acid template role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: realized in
  all values from: polymerase chain reaction
subclass of: Restriction
  on property: inheres in
  some values from: nucleic acid
example of usage: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
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.
editor preferred term: nucleic acid template role
has curation status: IAO_0000123

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
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Bjoern Peters
term editor: PERSON: Kevin Clancy
term editor: PERSON: Melanie Courtot
definition: a plasmid in which extraneous DNA has been inserted.
editor preferred term: recombinant plasmid
has curation status: IAO_0000120

cloning vector role
type: Class
subclass of: material to be added role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: nucleic acid
  intersection of: Restriction
    on property: realized in
    all values from: OBI_0600064
term editor: PERSON: Helen Parkinson
example of usage: pBluescript plays the role of a cloning vector
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/
editor preferred term: cloning vector role
has curation status: IAO_0000123

cell cycle synchronization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
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 transformation objective
definition source: Bjoern Peters and Nicole Washington
term editor: OBI PA
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.
definition: a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
editor preferred term: cell cycle synchronization
has curation status: IAO_0000120

polymerase chain reaction
type: Class
subclass of: OBI_0600058
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: realizes
  some values from: Class
    intersection of: synthesizing function
    intersection of: Restriction
      on property: inheres in
      some values from: DNA polymerase complex
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
term editor: OBI Plan
definition source: adapted from wikipedai
example of usage: Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
alternative term: PCR
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.
editor preferred term: polymerase chain reaction
has curation status: IAO_0000123

cloning insert role
type: Class
subclass of: role
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
editor preferred term: cloning insert role
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.
has curation status: IAO_0000121

measuring glucose concentration in blood serum
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: glucose
subclass 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
definition: An assay that determines the concentration of glucose molecules in a blood serum sample
term editor: Person:Bjoern Peters
editor preferred term: measuring glucose concentration in blood serum
has curation status: IAO_0000123

reverse transcriptase
type: Class
equivalent class: Class
  intersection of: enzyme
  intersection of: Restriction
    on property: has function
    some values from: RNA-directed DNA polymerase activity
subclass of: enzyme
definition source: group:OBI
term editor: person:Melanie Courtot
definition: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
editor preferred term: reverse transcriptase
has curation status: IAO_0000125

obsolete_trypsinized material
type: Class
subclass of: ObsoleteClass
definition: A material entity that has undergone a process of digestion with trypsin
example of usage: A trypsinized suspension of cells
term editor: Person:Bjoern Peters
editor note: decided to be deprecated on Aug 2, 2010 dev call
deprecated: true
curator note: Test Class: to evaluate OBI design pattern
editor preferred term: obsolete_trypsinized material
has curation status: IAO_0000002
has obsolescence reason: IAO_0000103

syringe
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
definition source: OBI Instrument adapted from Wikipedia
term editor: Philippe Rocca-Serra
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
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
editor preferred term: syringe
has curation status: IAO_0000122

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302884
definition source: GROUP: OBI Biomatrial Branch
term editor: PERSON: Philippe Rocca-Serra
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
definition: an extract is a material entity which results from an extraction process
editor preferred term: extract
alternative term: extracted material
has curation status: IAO_0000120

transcription profiling assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: transcription profiling identification objective
subclass of: analyte assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
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: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
definition source: OBI
term editor: Philippe Rocca-Serra
ISA alternative term: transcription profiling
definition: An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
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
alternative term: gene expression profiling
editor preferred term: transcription profiling assay
has curation status: IAO_0000120

averaging objective
type: Class
subclass of: OBI_0200166
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
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.
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: James Malone
editor preferred term: averaging objective
has curation status: IAO_0000122

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: inheres in
        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
definition source: OBI Biomaterial
term editor: Philippe Rocca-Serra
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
editor preferred term: injection
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.
has curation status: IAO_0000120

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acid
    union of: protein 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 complex
    union of: Restriction
      on property: has part
      some values from: PR_000000001
  intersection of: Restriction
    on property: has function
    some values from: catalytic activity
subclass of: material entity
definition source: GROUP:OBI
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: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
editor preferred term: enzyme
has curation status: IAO_0000125

intraperitoneal administration
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: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0002358
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: Person:Bjoern Peters
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
definition: The administration of a substance into the peritoneum of an organism
editor preferred term: intraperitoneal administration
has curation status: IAO_0000123

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
definition source: group:OBI
term editor: person:Melanie Courtot
editor preferred term: plasmid
definition: plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467
has curation status: IAO_0000125

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: inheres in
        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
definition: A process in which an input substance is injected into a organ section.
term editor: Person:Bjoern Peters
example of usage: Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
editor preferred term: injection into organ section
has curation status: IAO_0000123

polyacrylamide gel
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302890
subclass of: Restriction
  on property: has part
  some values from: acrylamide
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Jie Zheng
term editor: PERSON: Philippe Rocca-Serra
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
definition: a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
editor preferred term: polyacrylamide gel
has curation status: IAO_0000120

DNA sequence feature detection
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition: An assay with the objective to determine a sequence feature of DNA
definition source: OBI
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
example of usage: genotyping using an Affymetrix chip
editor preferred term: DNA sequence feature detection
editor note: should be a defined class where interpretation of data generated by assay qualifies a DNA sequence
has curation status: IAO_0000123

adding material objective
type: Class
subclass of: material combination objective
term editor: BP
example of usage: creating a mouse infected with LCM virus
editor preferred term: adding material objective
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
has curation status: IAO_0000122

genotyping assay
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: genotype information
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: genotype information
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: achieves_planned_objective
  some values from: sequence feature identification objective
definition source: OBI Biomaterial
term editor: Philippe Rocca-Serra
ISA alternative term: SNP analysis
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
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.
alternative term: genotype profiling, SNP genotyping
editor preferred term: genotyping assay
has curation status: IAO_0000120

needle
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
definition source: OBI Instrument
term editor: Philippe Rocca-Serra
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
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.
editor preferred term: needle
has curation status: IAO_0000120

analyte measurement objective
type: Class
subclass of: assay objective
term editor: PERSON: Bjoern Peters
definition source: PPPB branch
example of usage: The objective to measure the concentration of glucose in a blood sample
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
editor preferred term: analyte measurement objective
has curation status: IAO_0000122

DNA sequence variation detection
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition source: OBI Biomaterial
term editor: Philippe Rocca-Serra
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
editor preferred term: DNA sequence variation detection
definition: DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
has curation status: IAO_0000122

agarose gel
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302890
definition source: GROUP: OBI Biomaterial Branch
term editor: PERSON: Philippe Rocca-Serra
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
definition: a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
editor preferred term: agarose gel
has curation status: IAO_0000120

assay objective
type: Class
subclass of: objective specification
term editor: PPPB branch
definition source: PPPB branch
example of usage: the objective to determine the weight of a mouse.
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
editor preferred term: assay objective
has curation status: IAO_0000122

obsolete_heart
type: Class
subclass of: ObsoleteClass
example of usage: Alan Ruttenberg's heart
term editor: Person:Bjoern Peters
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
definition source: http://en.wikipedia.org/wiki/Heart
deprecated: true
editor note: unused class. decided to be deprecated on Aug 2, 2010 dev call. Will be imported when need.
editor note: MC: should be imported
editor preferred term: obsolete_heart
has curation status: IAO_0000002
has obsolescence reason: IAO_0000230

analyte assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: assay
subclass of: Restriction
  on property: realizes
  some values from: analyte role
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
definition source: PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
term editor: PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
editor note: logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
editor note: 2013-09-23: simplify equivalent axiom
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
editor note: Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
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

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
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
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.
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
editor preferred term: target of material addition role
has curation status: IAO_0000120

mass measurement assay
type: Class
subclass of: assay
subclass 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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: mass measurement datum
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
term editor: Helen Parkinson
definition source: OBI
comment: Philippe Rocca-Serra
example of usage: The patients was weighed and mass was determined to be 47 kilograms
definition: a process to determine the mass of an evaluant
editor preferred term: mass measurement assay
has curation status: IAO_0000120

obsolete_identification
type: Class
subclass of: ObsoleteClass
editor note: Alan Ruttenberg 2010/11/22: After OBI call. A specific identification objective should be used instead, as necessary
term editor: Philippe Rocca-Serra
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178
deprecated: true
example of usage: DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
definition: a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
editor preferred term: obsolete_identification
has obsolescence reason: IAO_0000103
has curation status: IAO_0000124

intra cellular electrophysiology recording
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: ion channel activity
definition: An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
term editor: PERSON: Frank Gibson
definition source: PERSON: Frank Gibson
editor preferred term: intra cellular electrophysiology recording
has curation status: IAO_0000123

packed column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218
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>
editor preferred term: packed column
has curation status: IAO_0000120

obsolete_defined_output
type: Class
subclass of: ObsoleteClass
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
deprecated: true
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.
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.
editor preferred term: obsolete_defined_output
has curation status: IAO_0000121
has obsolescence reason: IAO_0000226

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
term editor: GROUP: OBI Biomaterial Branch
example of usage: The US Environmental Protection Agency
definition source: WEB: en.wikipedia.org/wiki/Regulator
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.
editor preferred term: regulatory agency
has curation status: IAO_0000122

normalized data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200169
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
definition: A data set that is produced as the output of a normalization data transformation.
editor preferred term: normalized data set
has curation status: IAO_0000125

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
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson
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.
editor preferred term: measure function
has curation status: IAO_0000122

extracellular electrophysiology recording
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: ion channel activity
definition: An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
definition source: PERSON: Frank Gibson
term editor: PERSON: Frank Gibson, Helen Parkinson
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
editor preferred term: extracellular electrophysiology recording
has curation status: IAO_0000120

consume data function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: material entity
term editor: PERSON: Daniel Schober
term editor: PERSON: Frank Gibson
term editor: PERSON: Melanie Courtot
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.
editor preferred term: consume data function
has curation status: IAO_0000122

material transformation objective
type: Class
subclass of: objective specification
definition source: GROUP: OBI PlanAndPlannedProcess Branch
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
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
definition: an objective specifiction that creates an specific output object from input materials.
alternative term: artifact creation objective
editor preferred term: material transformation objective
has curation status: IAO_0000122

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_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
definition source: GROUP: OBI PlanAndPlannedProcess Branch
editor note: Manufacturing implies reproducibility and responsibility AR
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: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
editor note: This includes a single scientist making a processed material for personal use.
editor preferred term: manufacturing
has curation status: IAO_0000122

manufacturing objective
type: Class
subclass of: material transformation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
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: is the objective to manufacture a material of a certain function (device)
editor preferred term: manufacturing objective
has curation status: IAO_0000122

column chromatography detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
curator note: chromatography detector, defined class/xps
editor preferred term: column chromatography detector
has curation status: IAO_0000120

Bruker autosampler
type: Class
subclass of: autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209
definition: A Bruker autosampler is an autosampler made by Bruker.
editor preferred term: Bruker autosampler
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

organic acid column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: organic acid column
has curation status: IAO_0000120

thermal conductivity detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084
term editor: PERSON:Daniel Schober
alternative term: TCD, hot wire detector
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).
definition source: WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
editor preferred term: thermal conductivity detector
has curation status: IAO_0000120

Bruker US 2 NMR magnet
type: Class
subclass of: Bruker NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
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.
editor preferred term: Bruker US 2 NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
has curation status: IAO_0000120

protein column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: protein column
curator note: refactor as defined class
has curation status: IAO_0000120

solvent mixer
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: check on definition !
editor preferred term: solvent mixer
has curation status: IAO_0000120

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
definition: An assay that identifies the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
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.
definition source: Philippe Rocca-Serra
term editor: Philippe Rocca-Serra
editor preferred term: mass spectrometry assay
has curation status: IAO_0000120

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
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.
definition: a planned process that carries out a study design
definition: a planned process that realizes the concretization of a study design
definition source: branch derived
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to 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.
editor preferred term: study design execution
has curation status: IAO_0000122
imported from: Ontology for Biomedical Investigation

Bruker NMR Case sample changer
type: Class
subclass of: Bruker autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
editor preferred term: Bruker NMR Case sample changer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

nano pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052
definition: A pump system optimized for nano flow chromatography.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: nano pump system
has curation status: IAO_0000120

Bruker AutoClean system
type: Class
subclass of: NMR tube washing system
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205
editor preferred term: Bruker AutoClean system
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.
term editor: PERSON:Daniel Schober
editor note: washing system/NMR tube washing system, XPS: device has function washing
has curation status: IAO_0000120

manual injection system
type: Class
subclass of: sample injection system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
definition: The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
editor preferred term: manual injection system
has curation status: IAO_0000120

Varian GEMINI spectrometer
type: Class
subclass of: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
definition: An older Varian Broadband NMR spectrometer.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian GEMINI spectrometer
has curation status: IAO_0000120

column connector
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: column connector
has curation status: IAO_0000120

solid NMR probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
definition: An NMR probe that is designed to hold a solid sample.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: solid NMR probe
has curation status: IAO_0000120

Bruker high resolution probe
type: Class
subclass of: Bruker NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223
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.
editor preferred term: Bruker high resolution probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
alternative term: HR Probe
curator note: NMR probe
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

chromatography detector
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012
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>
editor preferred term: chromatography detector
has curation status: IAO_0000120

normal phase column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: normal phase column
has curation status: IAO_0000120

APOLLO console
type: Class
subclass of: tecmag NMR console
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
editor preferred term: APOLLO console
curator note: NMR instrument/NMR console
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.tecmag.com/apollo.htm>
has curation status: IAO_0000120

NMR sample holder
type: Class
subclass of: device
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
definition: An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
editor preferred term: NMR sample holder
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

chromatography instrument
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
definition: Any instrument that is used to carry out a chromatography experiment.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device, defined class?
editor preferred term: chromatography instrument
has curation status: IAO_0000120

continuous wave NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
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).
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
editor preferred term: continuous wave NMR instrument
has curation status: IAO_0000120

fourier transformation NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
definition source: GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
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.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: fourier transformation NMR instrument
has curation status: IAO_0000120

nitrogen phosphorous detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
editor preferred term: nitrogen phosphorous detector
has curation status: IAO_0000120

cation exchange column
type: Class
subclass of: ion exchange column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096
definition: A cation exchange column is a chromatography column that is used in cation exchange chromatography.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: cation exchange column
has curation status: IAO_0000120

direct detection NMR probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
definition: An NMR probe designed to allow the direct detection of acquisition nuclei.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: direct detection NMR probe
has curation status: IAO_0000120

Bruker B-ACS system
type: Class
subclass of: Bruker autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
editor preferred term: Bruker B-ACS system
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

rapid resolution column
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: rapid resolution column
has curation status: IAO_0000120

liquid chromatography autosampler
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061
definition: Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: liquid chromatography autosampler
has curation status: IAO_0000120

vacuum degasser
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053
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>
editor preferred term: vacuum degasser
has curation status: IAO_0000120

capillary column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066
definition: A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: capillary column
has curation status: IAO_0000120

sample inlet
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
curator note: chromatography device
editor preferred term: sample inlet
has curation status: IAO_0000120

NMR tube washing system
type: Class
subclass of: device
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
definition: An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
editor preferred term: NMR tube washing system
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

NMR console
type: Class
subclass of: device
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
definition: A component of an NMR instrument that controls the activities of the other components.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
editor preferred term: NMR console
curator note: NMR instrument, TODO: same as or part of acquisition computer?
term editor: PERSON:Daniel Schober
has curation status: IAO_0000125

dual loop autosampler
type: Class
subclass of: liquid chromatography autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063
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>
editor preferred term: dual loop autosampler
has curation status: IAO_0000120

variable wavelength detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079
definition: A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: variable wavelength detector
has curation status: IAO_0000120

Bruker LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
curator note: hyphenated NMR instrument platform
editor preferred term: Bruker LC-NMR platform
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
has curation status: IAO_0000120

sample injection system
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: sample injection system
has curation status: IAO_0000120

multiple wavelength detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078
definition: A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: multiple wavelength detector
has curation status: IAO_0000120

photoionization detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090
term editor: PERSON:Daniel Schober
alternative term: PID
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.
definition source: WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
editor preferred term: photoionization detector
has curation status: IAO_0000120

gas generator
type: Class
subclass of: gas chromatography equipment
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
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>
curator note: gas chromatography equipment
editor preferred term: gas generator
has curation status: IAO_0000120

column jacket
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: column jacket
has curation status: IAO_0000120

electron capture detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085
alternative term: ECD
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
editor preferred term: electron capture detector
has curation status: IAO_0000120

reversed phase column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: reversed phase column
has curation status: IAO_0000120

injector lubricant
type: Class
subclass of: chromatography consumable
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118
definition: A lubricant used in liquid chromatography that eases sample injector penetration.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: injector lubricant
has curation status: IAO_0000120

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
term editor: Person: Bjoern Peters
definition: a process in which a population of cells with certain characteristics is isolated from a larger population
editor preferred term: isolation of cell population
example of usage: removing CD4+ cells from PBMCs using magnetic beads.
has curation status: IAO_0000123

DISCOVERY console
type: Class
subclass of: tecmag NMR console
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
editor preferred term: DISCOVERY console
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument/NMR console
term editor: PERSON:Daniel Schober
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.
has curation status: IAO_0000120

Bruker AMX series NMR instrument
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
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.
editor preferred term: Bruker AMX series NMR instrument
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
has curation status: IAO_0000120

chromatofocusing column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209
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>
editor preferred term: chromatofocusing column
has curation status: IAO_0000120

NMR probe
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: part of
  some values from: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
editor preferred term: NMR probe
term editor: PERSON:Daniel Schober
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.
has curation status: IAO_0000120

NMR magnet
type: Class
subclass of: device
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
editor preferred term: NMR magnet
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

trap column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: trap column
has curation status: IAO_0000120

flow probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
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.
curator note: NMR device
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
editor preferred term: flow probe
has curation status: IAO_0000120

clinical chemistry assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: scattered molecular aggregate
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass 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
editor note: 3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid'
example of usage: Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M. Clin Chem Lab Med. 2008;46(4):558-62. PMID: 18605936
term editor: Person: Philippe Rocca-Serra
definition: a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism.
definition source: adapted from Wikipedia
alternative term: chemical pathology
ISA alternative term: clinical chemistry
editor preferred term: clinical chemistry assay
alternative term: detection of analyte in blood sample
has curation status: IAO_0000120

flame ionization detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197
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.
alternative term: FID
term editor: PERSON:Daniel Schober
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
editor preferred term: flame ionization detector
has curation status: IAO_0000120

vial
type: Class
subclass of: chromatography consumable
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117
definition: A vial is a cylindrical container often made from glass tubing.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: vial
has curation status: IAO_0000120

magic angle spinning rotor
type: Class
subclass of: device
subclass of: Restriction
  on property: part of
  some values from: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
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.
alternative term: MAS rotor
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.freepatentsonline.com/4352066.html>
editor preferred term: magic angle spinning rotor
has curation status: IAO_0000120

Varian VXR spectrometer
type: Class
subclass of: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
definition: A Varian NMR spectrometer.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian VXR spectrometer
definition source: WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
has curation status: IAO_0000120

splitless GC injector
type: Class
subclass of: sample injection system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060
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>
editor preferred term: splitless GC injector
has curation status: IAO_0000120

preparative autosampler
type: Class
subclass of: liquid chromatography autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062
definition: For preparative LC with injection of sample volumes ranging from L to mL ranges.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: preparative autosampler
has curation status: IAO_0000120

flow high resolution probe
type: Class
subclass of: Bruker high resolution probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
definition source: GROUP:<http://msi-ontology.sourceforge.net>
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.
curator note: NMR probe
term editor: PERSON:Daniel Schober
alternative term: flow HR-probe
editor preferred term: flow high resolution probe
has curation status: IAO_0000120

liquid chromatography valve
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
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>
curator note: chromatography device
editor preferred term: liquid chromatography valve
has curation status: IAO_0000120

JEOL NMR probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
definition: An NMR probe that is manufactured by JEOL.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
editor preferred term: JEOL NMR probe
curator note: NMR device
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker UltraShield Plus NMR magnet
type: Class
subclass of: Bruker NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
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.
editor preferred term: Bruker UltraShield Plus NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
has curation status: IAO_0000120

Bruker CryoProbe
type: Class
subclass of: Bruker NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
editor preferred term: Bruker CryoProbe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
term editor: PERSON:Daniel Schober
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 widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient.
has curation status: IAO_0000120

column cartridge
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055
definition: A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device, check on definition !
editor preferred term: column cartridge
has curation status: IAO_0000120

affinity column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: affinity column
has curation status: IAO_0000120

tecmag NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
definition: An NMR instrument that is manufactured by tecmag.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: tecmag NMR instrument
has curation status: IAO_0000120

gel filtration column
type: Class
subclass of: size exclusion column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: gel filtration column
has curation status: IAO_0000120

fraction collector
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073
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>
editor preferred term: fraction collector
has curation status: IAO_0000120

copy number variation profiling
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: genetic characteristics information
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
alternative term: CNV analysis
term editor: Philippe Rocca-Serra
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. de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796
editor preferred term: copy number variation profiling
definition: copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping.
has curation status: IAO_0000120

in-line filter
type: Class
subclass of: chromatography detector filter
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123
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>
editor preferred term: in-line filter
has curation status: IAO_0000120

imaging NMR probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
definition: An NMR probe that is designed for generating pictures from sample states via NMR imaging.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: imaging NMR probe
has curation status: IAO_0000120

isolation of adherent cells
type: Class
subclass of: isolation of cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
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.
editor preferred term: isolation of adherent cells
has curation status: IAO_0000123

Bruker AC series NMR instrument
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
definition: A series of older Bruker NMR magnets, now out of production.
editor preferred term: Bruker AC series NMR instrument
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

gas chromatography equipment
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
definition: Any device used in a gas chromatography experiment.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: gas chromatography equipment
curator note: will become defined class/xps
has curation status: IAO_0000120

syringe filter
type: Class
subclass of: chromatography detector filter
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122
definition: A small membrane filter of defined pore size, that filters samples from a syringe.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: syringe filter
has curation status: IAO_0000120

Bruker SampleRail system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207
editor preferred term: Bruker SampleRail system
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

column compartment
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: column compartment
has curation status: IAO_0000120

capillary pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051
definition: A pump system optimized for capillary chromatography.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: capillary pump system
has curation status: IAO_0000120

evaporative light scattering detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
editor preferred term: evaporative light scattering detector
has curation status: IAO_0000120

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: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100060
term editor: PERSON: bjoern peters
definition: a process in which cells with a single nucleus are isolated from a blood sample
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.
editor preferred term: isolation of PBMCs
definition source: wiki http://en.wikipedia.org/wiki/PBMC
has curation status: IAO_0000120

column cartridger
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054
definition: A chromatography device where the column cartridge is inserted into and stabilised.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: check on definition !
editor preferred term: column cartridger
has curation status: IAO_0000120

nitrogen generator
type: Class
subclass of: gas generator
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034
definition: A gas generator that generates nitrogen gas.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: nitrogen generator
has curation status: IAO_0000120

needle assembly
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
definition: The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
curator note: chromatography device, check on definition !
editor preferred term: needle assembly
has curation status: IAO_0000120

reverse transcribed polymerase chain reaction
type: Class
subclass of: OBI_0600058
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
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_output
  some values from: PCR product
editor note: 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
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
term editor: Philippe Rocca-Serra
alternative term: RT-PCR
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 preferred term: reverse transcribed polymerase chain reaction
alternative term: reverse transcription polymerase chain reaction
has curation status: IAO_0000123

Bruker Capillary LC-NMR platform
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
curator note: hyphenated NMR instrument platform
editor preferred term: Bruker Capillary LC-NMR platform
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.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
has curation status: IAO_0000120

gas chromatography oven
type: Class
subclass of: gas chromatography equipment
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: gas chromatography equipment
editor preferred term: gas chromatography oven
has curation status: IAO_0000120

autosampler
type: Class
subclass of: device
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: autosampler
has curation status: IAO_0000120

isocratic pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049
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>
editor preferred term: isocratic pump system
has curation status: IAO_0000120

flash pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048
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).
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: flash pump system
has curation status: IAO_0000120

Varian UNITY INOVA spectrometer
type: Class
subclass of: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
editor preferred term: Varian UNITY INOVA spectrometer
definition source: WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
has curation status: IAO_0000120

liquid NMR probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
definition: An NMR probe that is designed to hold a liquid sample.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: liquid NMR probe
has curation status: IAO_0000120

ion exchange column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: ion exchange column
has curation status: IAO_0000120

Bruker NMR probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231
definition: An NMR probe that is manufactured by Bruker.
editor preferred term: Bruker NMR probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device, TODO: May need no definition.
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

anion trap column
type: Class
subclass of: trap column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277
definition: An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: anion trap column
has curation status: IAO_0000120

fluorescene detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080
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>
editor preferred term: fluorescene detector
has curation status: IAO_0000120

tecmag EAGLE probe
type: Class
subclass of: solid NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
term editor: PERSON:Daniel Schober
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.
editor preferred term: tecmag EAGLE probe
has curation status: IAO_0000120

electrical conductivity detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
editor preferred term: electrical conductivity detector
has curation status: IAO_0000120

NMR instrument
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059
definition: An Instrument which is used to carry out a NMR analysis of some sample.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
alternative term: NMR instrument
curator note: NMR instrument
editor preferred term: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker UltraShield NMR magnet
type: Class
subclass of: Bruker NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
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.
editor preferred term: Bruker UltraShield NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

piston-seal
type: Class
subclass of: chromatography consumable
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
editor preferred term: piston-seal
has curation status: IAO_0000120

mass selective detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198
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
definition source: WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
editor preferred term: mass selective detector
alternative term: mass spectrometry detector
has curation status: IAO_0000120

spin column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: spin column
has curation status: IAO_0000120

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
term editor: GROUP: Role Branch
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
definition source: OBI
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.
editor preferred term: manufacturer role
has curation status: IAO_0000123

transfer line
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
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>
curator note: chromatography device
editor preferred term: transfer line
has curation status: IAO_0000120

gradient pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050
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>
editor preferred term: gradient pump system
has curation status: IAO_0000120

high temperature column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233
definition: A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: high temperature column
has curation status: IAO_0000120

Bruker Ultrastabilized NMR magnet
type: Class
subclass of: Bruker NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
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.
editor preferred term: Bruker Ultrastabilized NMR magnet
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

scattered molecular aggregate
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has grain
  all values from: molecular entity
subclass of: Restriction
  on property: has grain
  some values from: molecular entity
example of usage: the sodium and chloride ions in a glass of salt water
alternative term: 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
term editor: PERSON: Alan Ruttenberg
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
editor preferred term: scattered molecular aggregate
has curation status: IAO_0000123

obsolete_molecular concentration
type: Class
subclass of: ObsoleteClass
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.
definition source: Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
editor note: JZ: Can we replace the term by PATO: http://purl.obolibrary.org/obo/PATO_0000033 If not, we will wait the term available in PATO. Although specified that obsolete reason is 'term imported', the term has not imported yet. Will keep tracking this term until import the replaced term. Term depracted since the object property 'towards' used in the axioms is not avaliable in BFO2.
term editor: PERSON: Alan Ruttenberg
editor note: This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed. OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known. Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist.
editor note: logical definition in OBI: 'quality of related physical entities' ('inheres in' some material_entity) and (towards some 'scattered molecular aggregate')
example of usage: the phosphate concentration should be 0.1M
deprecated: true
editor preferred term: obsolete_molecular concentration
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

NMR sample tube
type: Class
subclass of: test tube
subclass of: Restriction
  on property: part of
  some values from: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
editor preferred term: NMR sample tube
term editor: PERSON:Daniel Schober
definition: The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
has curation status: IAO_0000120

Varian UNITY spectrometer
type: Class
subclass of: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition: The predecessor series of the Varian UNITY INOVA spectrometer.
editor preferred term: Varian UNITY spectrometer
definition source: WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
has curation status: IAO_0000120

AVANCE II spectrometer
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
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.
editor preferred term: AVANCE II spectrometer
curator note: NMR instrument
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>
has curation status: IAO_0000120

y-column connector
type: Class
subclass of: column connector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237
definition: A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: y-column connector
has curation status: IAO_0000120

Bruker LC-NMR/MS platform
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
curator note: hyphenated NMR instrument platform
editor preferred term: Bruker LC-NMR/MS platform
definition source: GROUP:<http://msi-ontology.sourceforge.net>
definition: Includes the connection to a high-resolution TOF-LC-MS system.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

refractive index detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081
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>
editor preferred term: refractive index detector
has curation status: IAO_0000120

anion exchange column
type: Class
subclass of: ion exchange column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095
definition: An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: anion exchange column
has curation status: IAO_0000120

plunger column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: plunger column
has curation status: IAO_0000120

flame photometric detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091
alternative term: FPD
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
editor preferred term: flame photometric detector
has curation status: IAO_0000120

chromatography pump system
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046
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>
editor preferred term: chromatography pump system
has curation status: IAO_0000120

Bruker 1mm MicroProbe
type: Class
subclass of: Bruker NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
editor preferred term: Bruker 1mm MicroProbe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
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 properties\n virtually no salt effect\n discrete samples in tubes that can be sealed and stored\n automation accessory for sample preparation and handling available.
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker BEST NMR system
type: Class
subclass of: Bruker autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
editor preferred term: Bruker BEST NMR system
alternative term: Bruker Efficient Sample Transfer NMR
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

chromatography detector filter
type: Class
subclass of: chromatography consumable
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121
definition: An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: chromatography detector filter
has curation status: IAO_0000120

cation trap column
type: Class
subclass of: trap column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278
definition: A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: cation trap column
has curation status: IAO_0000120

column adapter
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
definition: An Adapter that enabled the connection of a column to additional devices.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
curator note: chromatography device
editor preferred term: column adapter
has curation status: IAO_0000120

pulsed amperometric detector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240
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).
alternative term: PAD
term editor: PERSON:Daniel Schober
definition source: WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
editor preferred term: pulsed amperometric detector
has curation status: IAO_0000120

Bruker NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198
definition: An NMR instrument that is manufactured by Bruker.
editor preferred term: Bruker NMR instrument
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

Bruker NMR magnet
type: Class
subclass of: NMR magnet
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186
definition: An NMR magnet that is manufactured by Bruker.
editor preferred term: Bruker NMR magnet
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

ozone-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088
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>
editor preferred term: ozone-induced chemiluminescence detector
has curation status: IAO_0000120

tecmag NMR console
type: Class
subclass of: NMR console
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
definition: An NMR console manufactured by tecmac.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: tecmag NMR console
has curation status: IAO_0000120

JEOL NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226
definition: An NMR instrument that is manufactured by JEOL.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
editor preferred term: JEOL NMR instrument
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

chromatography consumable
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
definition: A chromatography consumable is a consumable that is used in a chromatography experiment.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: chromatography consumable
curator note: chromatography device
has curation status: IAO_0000120

column frit
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
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>
curator note: chromatography device
editor preferred term: column frit
has curation status: IAO_0000120

liquid chromatography column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: liquid chromatography column
has curation status: IAO_0000120

detector lamp
type: Class
subclass of: chromatography consumable
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119
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>
editor preferred term: detector lamp
has curation status: IAO_0000120

chart recorder
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
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.
editor preferred term: chart recorder
curator note: chromatography device
has curation status: IAO_0000120

open tubular column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219
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>
editor preferred term: open tubular column
has curation status: IAO_0000120

high resolution magic angle spin probe
type: Class
subclass of: Bruker high resolution probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR probe
term editor: PERSON:Daniel Schober
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.
alternative term: high resolution MAS, hr-MAS
editor preferred term: high resolution magic angle spin probe
has curation status: IAO_0000120

hydrogen generator
type: Class
subclass of: gas generator
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035
definition: A gas generator that generates hydrogen gas.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: hydrogen generator
has curation status: IAO_0000120

glass column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101
definition: A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: glass column
has curation status: IAO_0000120

auto injector
type: Class
subclass of: sample injection system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058
definition: A gas chromatography device that can auto-inject a small number of samples an inlet.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: auto injector
has curation status: IAO_0000120

Varian NMR instrument
type: Class
subclass of: NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234
definition: An NMR instrument that is manufactured by Varian.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian NMR instrument
has curation status: IAO_0000120

Bruker MATCH tube holder system
type: Class
subclass of: NMR sample holder
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
editor preferred term: Bruker MATCH tube holder system
alternative term: Bruker Multiple Adjustable Tube Clamp Holder
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
has curation status: IAO_0000120

Bruker SPE-NMR platform
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
curator note: hyphenated NMR instrument platform
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.
editor preferred term: Bruker SPE-NMR platform
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
has curation status: IAO_0000120

guard column
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
definition source: GROUP:<http://msi-ontology.sourceforge.net>
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
curator note: chromatography device
editor preferred term: guard column
has curation status: IAO_0000120

protein expression profiling
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
definition source: OBI branch derived
term editor: Phlippe Rocca-Serra
example of usage: Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ. Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203
definition: a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays
editor preferred term: protein expression profiling
alternative term: proteomic analysis
has curation status: IAO_0000120

high resolution probe with automatic tuning and matching
type: Class
subclass of: Bruker high resolution probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
definition source: GROUP:<http://msi-ontology.sourceforge.net>
alternative term: High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
curator note: NMR probe
term editor: PERSON:Daniel Schober
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.
editor preferred term: high resolution probe with automatic tuning and matching
has curation status: IAO_0000120

fluorine-induced chemiluminescence detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087
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>
editor preferred term: fluorine-induced chemiluminescence detector
has curation status: IAO_0000120

size exclusion column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: size exclusion column
has curation status: IAO_0000120

chromatography splitter
type: Class
subclass of: chromatography device
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
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>
curator note: chromatography device
editor preferred term: chromatography splitter
has curation status: IAO_0000120

Bruker micro imaging probe
type: Class
subclass of: Bruker NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
editor preferred term: Bruker micro imaging probe
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.
curator note: NMR probe
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
has curation status: IAO_0000120

custom made column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: custom made column
has curation status: IAO_0000120

gel permeation column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103
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>
editor preferred term: gel permeation column
has curation status: IAO_0000120

NMR spectroscopy
type: Class
subclass of: assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
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
editor preferred term: NMR spectroscopy
definition: NMR spectroscopy is a process which 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.
alternative term: Nuclear magnetic resonance spectroscopy
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia
has curation status: IAO_0000123

Bruker SampleJet system
type: Class
subclass of: Bruker autosampler
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
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.
editor preferred term: Bruker SampleJet system
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/automation.html>
has curation status: IAO_0000120

JEOL ECX NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
editor preferred term: JEOL ECX NMR spectrometer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
has curation status: IAO_0000120

DNA sequencing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: deoxyribonucleic acid
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
  intersection of: Restriction
    on property: has_specified_output
    some values from: DNA sequence data
subclass of: OBI_0600047
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
editor preferred term: DNA sequencing
definition: DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
example of usage: Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
definition source: OBI Branch derived
term editor: Philippe Rocca-Serra
ISA alternative term: nucleotide sequencing
has curation status: IAO_0000123

quaternary pump system
type: Class
subclass of: chromatography pump system
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047
definition: A pump system that pump and mix up to four different solvents in parallel.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
term editor: PERSON:Daniel Schober
editor preferred term: quaternary pump system
has curation status: IAO_0000120

carbon nanotube column
type: Class
subclass of: chromatography column
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107
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>
editor preferred term: carbon nanotube column
has curation status: IAO_0000120

Bruker solid magic angle spinning probe
type: Class
subclass of: Bruker NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
editor preferred term: Bruker solid magic angle spinning probe
definition source: GROUP:<http://msi-ontology.sourceforge.net>
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.
curator note: NMR probe
term editor: PERSON:Daniel Schober
alternative term: solid MAS probe
has curation status: IAO_0000120

hematology
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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943
definition source: OBI branch derived
term editor: Philippe Rocca-Serra
alternative term: blood analysis, haematology
editor preferred term: hematology
definition: hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
has curation status: IAO_0000123

Varian MERCURY spectrometer
type: Class
subclass of: Varian NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
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.
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: Varian MERCURY spectrometer
has curation status: IAO_0000120

Bruker Metabolic Profiler
type: Class
subclass of: Bruker NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
curator note: hyphenated NMR instrument platform
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.
editor preferred term: Bruker Metabolic Profiler
curator note: NMR instrument
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
has curation status: IAO_0000120

column heater
type: Class
subclass of: chromatography instrument
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
editor preferred term: column heater
has curation status: IAO_0000120

DNA methylation profiling assay
type: Class
equivalent class: 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: regulation of DNA methylation
subclass of: analyte assay
subclass of: OBI_0002020
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      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
ISA alternative term: DNA methylation profiling
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. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
definition source: OBI branch derived
term editor: Philippe Rocca-Serra
definition: an assay which aims to provide information about 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.
has curation status: IAO_0000122

JEOL CapNMR probe
type: Class
subclass of: JEOL NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
editor preferred term: JEOL CapNMR probe
curator note: NMR probe
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
has curation status: IAO_0000120

acquisition computer
type: Class
subclass of: OBI_0400107
subclass of: Restriction
  on property: has function
  some values from: information processor function
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
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.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR instrument
term editor: PERSON:Daniel Schober
editor preferred term: acquisition computer
has curation status: IAO_0000120

gas chromatography detector
type: Class
subclass of: chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
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.
alternative term: FID
term editor: PERSON:Daniel Schober
definition source: WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
curator note: chromatography detector, defined class/xps
editor preferred term: gas chromatography detector
has curation status: IAO_0000120

gas purifier
type: Class
subclass of: gas chromatography equipment
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
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>
curator note: gas chromatography equipment
editor preferred term: gas purifier
has curation status: IAO_0000120

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
definition source: PPPB branch
term editor: PPPB branch
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
definition: is an objective to transform a material entity into spatially separated components.
editor preferred term: material separation objective
has curation status: IAO_0000122

indirect detection probe
type: Class
subclass of: NMR probe
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
definition: An NMR probe designed to allow the indirect detection of acquisition nuclei.
definition source: GROUP:<http://msi-ontology.sourceforge.net>
curator note: NMR device
term editor: PERSON:Daniel Schober
editor preferred term: indirect detection probe
has curation status: IAO_0000120

JEOL ECA NMR spectrometer
type: Class
subclass of: JEOL NMR instrument
definition source: http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
editor preferred term: JEOL ECA NMR spectrometer
curator note: NMR instrument
term editor: PERSON:Daniel Schober
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.
definition source: WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
has curation status: IAO_0000120

atomic emission detector
type: Class
subclass of: gas chromatography detector
definition source: http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086
alternative term: AED
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
definition source: WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
editor preferred term: atomic emission detector
has curation status: IAO_0000120

clustered data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200175
subclass of: data set
example of usage: A clustered data set is the output of a K means clustering data transformation
curator note: AR thinks could be a data item instead
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned discovered class labels
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.
editor preferred term: clustered data set
has curation status: IAO_0000125

data set of features
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200184
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
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.
editor preferred term: data set of features
has curation status: IAO_0000125

differential expression analysis data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200031
subclass of: OBI_0200000
definition: A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
term editor: James Malone
term editor: Melanie Courtot
term editor: Monnie McGee
definition source: WEB:
editor preferred term: differential expression analysis data transformation
has curation status: IAO_0000122

urine specimen
type: Class
subclass of: specimen from organism
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600005
subclass of: Restriction
  on property: derives from
  some values from: UBERON_0001088
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
definition: a portion of urine collected from an organism
editor note: are we happy calling collection of urine a material separation?
editor preferred term: urine specimen
has curation status: IAO_0000120

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
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
definition source: bp
term editor: bp
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
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 preferred term: material combination
has curation status: IAO_0000122

fuzzy clustering objective
type: Class
subclass of: OBI_0200166
definition source: PERSON: James Malone
definition source: PERSON: Ryan Brinkman
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
editor preferred term: fuzzy clustering objective
has curation status: IAO_0000122

device setting
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: processed material
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
term editor: PERSON: Frank Gibson
definition: a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
editor preferred term: device setting
has curation status: IAO_0000123

blood specimen
type: Class
subclass of: specimen from organism
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600005
subclass of: Restriction
  on property: derives from
  some values from: UBERON_0000178
definition source: Bjoern Peters
term editor: Bjoern Peters
definition: a material entity derived from a portion of blood collected from an organism
example of usage: blood drawn from a human for glucose assay
editor preferred term: blood specimen
has curation status: IAO_0000122

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
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
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.
editor preferred term: data set of predicted values according to fitted curve
has curation status: IAO_0000125

data representational model
type: Class
subclass of: directive information entity
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
definition: Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
definition source: GROUP: OBI
term editor: Melanie Courtot
editor preferred term: data representational model
alternative term: data structure
alternative term: data structure specification
example of usage: gene regulatory graph model
example of usage: phylogenetic tree
example of usage: protein interaction network
has curation status: IAO_0000120

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_output
  some values from: OBI_0100051
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
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
definition: A planned process with the objective of collecting a specimen.
term editor: Bjoern Peters
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 preferred term: specimen collection process
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.
alternative term: specimen collection
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/
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
has curation status: IAO_0000122

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
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
definition: A data set that is produced as the output of a background correction data transformation.
editor preferred term: background corrected data set
has curation status: IAO_0000125

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: inheres in
        some values from: immunoglobulin complex, circulating
  intersection of: Restriction
    on property: has_specified_input
    some values from: immunoglobulin complex, circulating
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.
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.
alternative term: ELISA
term editor: IEDB
definition source: IEDB
editor preferred term: enzyme-linked immunosorbent assay
has curation status: IAO_0000120

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
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
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).
editor preferred term: error corrected data set
has curation status: IAO_0000125

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
term editor: James Malone
alternative term: supervised classification data transformation
definition: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
definition source: PERSON: James Malone
editor preferred term: class prediction data transformation
has curation status: IAO_0000122

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: REO_0000171
      intersection of: Restriction
        on property: inheres in
        some values from: 5-bromo-2'-deoxyuridine
  intersection of: Restriction
    on property: has_specified_input
    some values from: 5-bromo-2'-deoxyuridine
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.
editor preferred term: BrdU incorporation assay
term editor: IEDB
definition source: IEDB
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

obsolete intracellular cytokine staining assay
type: Class
subclass of: ObsoleteClass
alternative term: ICS
alternative term: ICCS
definition source: IEDB
term editor: IEDB
example of usage: Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
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.
IEDB alternative term: intracellular cytokine staining (ICS)
editor preferred term: obsolete intracellular cytokine staining assay
deprecated: true
has curation status: IAO_0000120
has obsolescence reason: IAO_0000227
term replaced by: flow cytometry assay

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
term editor: James Malone
definition: A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
definition source: PERSON: James Malone
editor preferred term: background correction data transformation
has curation status: IAO_0000122

obsolete MHC multimer staining assay
type: Class
subclass of: ObsoleteClass
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
definition source: IEDB
term editor: IEDB
alternative term: MHC tetramer assay
IEDB alternative term: MHC tetramer/multimer staining
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.
editor preferred term: obsolete MHC multimer staining assay
deprecated: true
has curation status: IAO_0000120
has obsolescence reason: IAO_0000227
term replaced by: OBI_1110179

error correction data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200186
subclass of: OBI_0200000
definition source: EDITORS
term editor: Monnie McGee
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
editor preferred term: error correction data transformation
has curation status: IAO_0000122

tritiated thymidine incorporation assay
type: Class
subclass of: cell proliferation assay
subclass of: Restriction
  on property: has part
  some values from: radioactivity detection
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: REO_0000171
      intersection of: Restriction
        on property: inheres in
        some values from: tritiated thymidine
  intersection of: Restriction
    on property: has_specified_input
    some values from: tritiated thymidine
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.
definition source: IEDB
term editor: IEDB
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.
editor preferred term: tritiated thymidine incorporation assay
has curation status: IAO_0000120

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600005
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: UBERON_0000465
editor note: 5/29: This is a helper class for now
definition: a material obtained from an organism in order to be a representative of the whole
editor preferred term: sample from organism
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.
has curation status: IAO_0000002

statistical hypothesis test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: OBI_0200000
term editor: James Malone
definition: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
definition source: PERSON: James Malone
editor preferred term: statistical hypothesis test
has curation status: IAO_0000120

center value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200181
subclass of: data item
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: median
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.
editor preferred term: center value
has curation status: IAO_0000125

statistical hypothesis test objective
type: Class
subclass of: OBI_0200166
term editor: Person:Helen Parkinson
definition source: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
alternative term: hypothesis test objective
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
editor preferred term: statistical hypothesis test objective
has curation status: IAO_0000123

reduced dimension data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200182
subclass of: data set
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
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.
editor preferred term: reduced dimension data set
has curation status: IAO_0000125

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
editor preferred term: portioning objective
has curation status: IAO_0000123

average value
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: OBI_0200170
subclass of: data item
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: arithmetic mean
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
editor preferred term: average value
has curation status: IAO_0000125

whole organism preparation
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: derives from
  some values from: OBI_0100026
subclass of: Restriction
  on property: is_specified_output_of
  some values from: specimen collection process
subclass of: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
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.
example of usage: putting a mouse in the blender. Not: putting a mouse on a scale
editor preferred term: whole organism preparation
has curation status: IAO_0000123

separation into different composition objective
type: Class
subclass of: material separation objective
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).
example of usage: The objective to obtain cells contained in a sample of blood.
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
editor preferred term: separation into different composition objective
has curation status: IAO_0000120

obsolete_study result
type: Class
subclass of: ObsoleteClass
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
definition source: GROUP: OBI
definition: Study result is an information content entity that is a specified data output of a study.
editor preferred term: obsolete_study result
deprecated: true
has curation status: IAO_0000120
has obsolescence reason: IAO_0000230

specimen collection objective
type: Class
subclass of: objective specification
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
editor preferred term: specimen collection objective
has curation status: IAO_0000122

creating a mixture of molecules in solution
type: Class
subclass of: material combination
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
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
term editor: Bjoern Peters
definition source: PERSON: Helen Parkinson
example of usage: The production of PBS
editor preferred term: creating a mixture of molecules in solution
definition: is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
has curation status: IAO_0000120

material combination objective
type: Class
subclass of: material transformation objective
term editor: PPPB branch
definition source: bp
definition: is an objective to obtain an output material that contains several input materials.
editor preferred term: material combination objective
has curation status: IAO_0000122

nucleotide overhang cloning
type: Class
subclass of: OBI_0600064
example of usage: Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
term editor: Helen Parkinson
definition: Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
editor preferred term: nucleotide overhang cloning
has curation status: IAO_0000120

rodent care protocol
type: Class
subclass of: animal care protocol
definition: A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
definition source: Bjoern Peters
term editor: Bjoern Peters
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.
editor preferred term: rodent care protocol
has curation status: IAO_0000123

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
alternative term: GS 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.
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by 454 Life Science Corporation 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.
has curation status: IAO_0000120

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
definition source: OBI plan and planned process branch
example of usage: PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
term editor: Philippe Rocca-Serra
editor preferred term: immunoprecipitation
definition: is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
has curation status: IAO_0000123

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
definition source: Applied Biosystems
term editor: Philippe Rocca-Serra
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.
has curation status: IAO_0000120

recombination enzyme based cloning
type: Class
subclass of: OBI_0600064
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
editor preferred term: recombination enzyme based cloning
has curation status: IAO_0000123

MeDIP-seq assay
type: Class
subclass of: DNA methylation profiling assay
subclass of: OBI_0001956
subclass of: OBI_0600047
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: deoxyribonucleic acid
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: has part
  some values from: immunoprecipitation
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: primary structure of DNA macromolecule
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: regulation of DNA methylation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: Helicos sequencing
    union of: SOLiD sequencing
    union of: Solexa sequencing
    union of: pyrosequencing
editor preferred term: MeDIP-seq assay
alternative term: Methylated DNA immunoprecipitation sequencing 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, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia
definition: is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on 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.
has curation status: IAO_0000120

animal feeding
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0100026
subclass of: Restriction
  on property: realizes
  some values from: feed role
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100026
term editor: Bjoern Peters
editor note: In an investigation, this will typically be part of an animal care process
editor preferred term: animal feeding
definition: animal feeding is a process in which animals are provided with food
definition source: branch derived
example of usage: giving crickets to a snake.
has curation status: IAO_0000123

chain termination sequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: has_specified_input
  some values from: PCR product
subclass of: Restriction
  on property: has participant
  some values from: Class
    union of: ABI 377 automated sequencer
    union of: Li-Cor 4300 DNA Analysis System
example of usage: PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.
term editor: Philippe Rocca-Serra
alternative term: Sanger sequencing
definition source: adapted from wikipedia
editor preferred term: chain termination sequencing
alternative term: dye terminator sequencing
definition: is a DNA sequencing 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
has curation status: IAO_0000120

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
definition source: Applied Biosystems
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.
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
has curation status: IAO_0000120

Helicos sequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: has participant
  some values from: HeliScope Single Molecule Sequencer
subclass of: Restriction
  on property: immediately preceded by
  some values from: OBI_0302902
editor preferred term: Helicos sequencing
example of usage: PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia
definition: is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length.
alternative term: true single molecule sequencing
has curation status: IAO_0000120

obsolete_DNA ligase
type: Class
subclass of: ObsoleteClass
editor note: 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
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 term: ligase
editor preferred term: obsolete_DNA ligase
editor note: replaced by imported PRO: DNA ligase
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

survival assessment
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: Class
    intersection of: survival rate
    intersection of: Restriction
      on property: is about
      some values from: OBI_0100026
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor note: Need to point out more specifically that survival / death is measured.
definition: Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
editor preferred term: survival assessment
has curation status: IAO_0000123

support vector machine
type: Class
subclass of: class prediction data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200179
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
definition source: PERSON: Ryan Brinkman
term editor: Ryan Brinkman
alternative term: SVM
editor preferred term: support vector machine
has curation status: IAO_0000123

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
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
definition source: PERSON: Ryan Brinkman
term editor: Ryan Brinkman
alternative term: SOM
editor preferred term: self-organizing map
has curation status: IAO_0000125

454 Genome Sequencer FLX
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000758
alternative term: 454 GS FLX
editor preferred term: 454 Genome Sequencer FLX
alternative term: GS-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.
term editor: Philippe Rocca-Serra
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
definition: is a DNA sequencer which is manufactured by 454 Life Science Corporation 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.
has curation status: IAO_0000120

Illumina Genome Analyzer II
type: Class
subclass of: OBI_0400103
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000759
definition source: Illumina Corporation
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.
term editor: Philippe Rocca-Serra
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
has curation status: IAO_0000120

decision tree induction objective
type: Class
subclass of: OBI_0200166
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
editor preferred term: decision tree induction objective
has curation status: IAO_0000123

Edman degradation
type: Class
subclass of: OBI_0600047
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: SO_0000104
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: REO_0000171
      intersection of: Restriction
        on property: inheres in
        some values from: material entity
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
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.
example of usage: Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT.
editor preferred term: Edman degradation
definition source: IEDB
term editor: IEDB
has curation status: IAO_0000120

SOLiD sequencing
type: Class
subclass of: DNA sequencing by ligation
subclass of: Restriction
  on property: has participant
  some values from: AB SOLiD System
subclass of: Restriction
  on property: immediately preceded by
  some values from: Class
    intersection of: OBI_0302902
    intersection of: Restriction
      on property: immediately preceded by
      some values from: OBI_0600048
subclass of: Restriction
  on property: has_specified_input
  some values from: PR_000023089
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: paired-end library
    union of: single fragment library
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.
term editor: Philippe Rocca-Serra
editor preferred term: SOLiD sequencing
definition source: adapted from Wikipedia and Applied Biosystems web site
definition: is a DNA sequencing which allows sequence identification by relying on the following steps: 1. Primers hybridize to the P1 adapter sequence within the library template. 2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. 3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. 4. 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
has curation status: IAO_0000120

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
term editor: James Malone
definition: A decision tree building data transformation is a data transformation that has objective decision tree induction.
definition source: PERSON: James Malone
editor preferred term: decision tree building data transformation
has curation status: IAO_0000120

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
definition: a process that realizes an animal care protocol that specifies how animals are kept and maintained
editor preferred term: laboratory animal care
has curation status: IAO_0000123

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
term editor: Kevin Clancy, Bjoern Peters
alternative term: YAC
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
editor preferred term: yeast artificial chromosome vector
has curation status: IAO_0000123

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
definition source: OBI and Li-Cor
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
has curation status: IAO_0000120

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: 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
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.
term editor: Philippe Rocca-Serra
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.
alternative term: library construction
editor preferred term: library preparation
has curation status: IAO_0000120

pathogen challenge
type: Class
subclass of: OBI_0600007
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
definition: A pathogen challenge is the administration of a live pathogenic organism to a host
editor preferred term: pathogen challenge
has curation status: IAO_0000123

GenePattern software
type: Class
subclass of: software
editor preferred term: GenePattern software
term editor: James Malone
term editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
has curation status: IAO_0000120

graph of vertices
type: Class
subclass of: graph
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
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.
term editor: James Malone
definition source: WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
editor preferred term: graph of vertices
has curation status: IAO_0000123

animal care protocol
type: Class
subclass of: protocol
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
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.
editor preferred term: animal care protocol
has curation status: IAO_0000123

ChIP-seq assay
type: Class
subclass of: OBI_0001956
subclass of: OBI_0002020
subclass of: OBI_0600047
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: OBI_0100051
    intersection of: Class
      intersection of: Restriction
        on property: has part
        some values from: deoxyribonucleic acid
      intersection of: Restriction
        on property: has part
        some values from: protein complex
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: Class
        union of: chromatin remodeling
        union of: regulation of molecular function, epigenetic
        union of: sequence-specific DNA binding
        union of: transcription factor binding site
subclass of: Restriction
  on property: has part
  some values from: immunoprecipitation
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
subclass of: Restriction
  on property: has_specified_output
  some values from: DNA sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: has part
  some values from: library preparation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: protein and DNA interaction identification objective
subclass of: Restriction
  on property: has part
  some values from: DNA sequencing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: deoxyribonucleic acid
editor preferred term: ChIP-seq assay
example of usage: PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia
definition: an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
alternative term: chromatin immunoprecipitation sequencing assay
curator note: made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes
has curation status: IAO_0000122

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
term editor: Philippe Rocca-Serra
definition: is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
has curation status: IAO_0000120

pathogen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0100026
subclass of: Restriction
  on property: realized in
  all values from: OGMS_0000063
curator note: 6 April 2009: from the Vaccine Community
term editor: GROUP: Role Branch
definition source: OBI
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
editor preferred term: pathogen role
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
has curation status: IAO_0000120

vaccine preparation
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition source: OBI
example of usage: The production of B. pertussis vaccine.
editor preferred term: vaccine preparation
definition: vaccine preparation is a planned process with specified output a vaccine
has curation status: IAO_0000120

immunologic adjuvant role
type: Class
subclass of: OBI_1110092
subclass of: Restriction
  on property: realized in
  all values from: immune response
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'.
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
term editor: GROUP: Role branch
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
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.
definition source: Vaccine Ontology, Wikipedia, OBI
editor preferred term: immunologic adjuvant role
has curation status: IAO_0000120

glucose tolerance test
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: measuring glucose concentration in blood serum
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: study design dependent variable
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: biological feature identification objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: information content entity
    intersection of: Restriction
      on property: is_proxy_for
      some values from: Insulin resistance
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0600007
    intersection of: Restriction
      on property: has_specified_input
      some values from: glucose
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: OBI_0200000
    intersection of: Restriction
      on property: has_specified_input
      some values from: measurement datum
    intersection of: Restriction
      on property: has_specified_output
      some values from: graph
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: study design independent variable
definition source: NuGO OBI plan branch
example of usage: PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9.
term editor: Philippe Rocca-Serra
editor preferred term: glucose tolerance test
definition: is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
editor note: 30-10-2013:[author: PRS] removing "realizes some (concretizes some 'time series design')" axiom as it causes 'gtt' to be classified under study design execution instead of assay
has curation status: IAO_0000122

paired-end library
type: Class
subclass of: processed material
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.
term editor: Philippe Rocca-Serra
definition source: adapted from information provided by Solid web site
definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
alternative term: mate-paired library
editor preferred term: paired-end library
alternative term: paired-end tag (PET) library
has curation status: IAO_0000123

DNA sequencing by ligation
type: Class
subclass of: DNA sequencing
subclass of: Restriction
  on property: has_specified_input
  some values from: PR_000023089
editor preferred term: DNA sequencing by ligation
editor note: PERSON: Philippe Rocca-Serra
example of usage: PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
definition: is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
has curation status: IAO_0000123

Solexa sequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: immediately preceded by
  some values from: Class
    intersection of: OBI_0302902
    intersection of: Restriction
      on property: immediately preceded by
      some values from: OBI_0600048
subclass of: Restriction
  on property: has participant
  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
example of usage: PMID: 18987734 Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP,…
term editor: Philippe Rocca-Serra
editor preferred term: Solexa sequencing
definition source: adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
definition: is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow 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.
alternative term: reversible terminator sequencing
has curation status: IAO_0000120

host role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: OBI_0100026
definition source: 30 Mar09 submitted by vaccine community
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
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
definition source: OBI
editor preferred term: host role
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
definition source: http://en.wikipedia.org/wiki/Host_(biology)
has curation status: IAO_0000120

peak matching
type: Class
subclass of: OBI_0200000
term editor: James Malone
definition source: PERSON: Ryan Brinkman
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: Ryan Brinkman
editor preferred term: peak matching
has curation status: IAO_0000123

k-nearest neighbors
type: Class
subclass of: OBI_0200171
subclass of: OBI_0200175
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200172
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
alternative term: k-NN
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
definition source: PERSON: James Malone
editor preferred term: k-nearest neighbors
has curation status: IAO_0000125

rodent care
type: Class
subclass of: laboratory animal care
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: contain function
    intersection of: Restriction
      on property: inheres in
      some values from: OBI_0400171
subclass of: Restriction
  on property: has_specified_input
  some values from: Rodentia
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 part
  some values from: animal feeding
subclass of: Restriction
  on property: has_specified_output
  some values from: Rodentia
term editor: PPPB branch
definition source: PPPB branch
example of usage: keeping animal
editor preferred term: rodent care
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.
has curation status: IAO_0000123

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
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
editor preferred term: cloning plasmid
has curation status: IAO_0000123

pyrosequencing
type: Class
subclass of: DNA sequencing by synthesis
subclass of: Restriction
  on property: has participant
  some values from: Class
    union of: 454 Genome Sequence 20
    union of: 454 Genome Sequencer FLX
term editor: Philippe Rocca-Serra
example of usage: Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
definition source: Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
definition: is a DNA sequencing which allows sequencing of 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.
editor preferred term: pyrosequencing
has curation status: IAO_0000120

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
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.
editor preferred term: recombinant vector
has curation status: IAO_0000123

restriction enzyme
type: Class
subclass of: enzyme
subclass of: PR_000000001
subclass of: Restriction
  on property: has function
  some values from: catalytic activity
curator note: 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
term editor: Kevin Clancy, Bjoern Peters
example of usage: The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
definition: an enzyme that has a specific target cleavage sites within nucleic acids
editor preferred term: restriction enzyme
has curation status: IAO_0000123

DNA sequencing by synthesis
type: Class
subclass of: DNA sequencing
subclass of: Restriction
  on property: has_specified_input
  some values from: DNA polymerase complex
editor preferred term: DNA sequencing by synthesis
term editor: PERSON: Philippe Rocca-Serra
example of usage: PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25.
definition: is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
has curation status: IAO_0000123

NTP-2000
type: Class
subclass of: processed material
subclass of: Restriction
  on property: has role
  some values from: feed role
subclass of: Restriction
  on property: is_specified_output_of
  some values from: manufacturing
term editor: Jennifer Fostel, Bjoern Peters
editor preferred term: NTP-2000
definition: a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
has curation status: IAO_0000123

single fragment library
type: Class
subclass of: processed material
term editor: Philippe Rocca-Serra
alternative term: fragment library
definition: is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
editor preferred term: single fragment library
has curation status: IAO_0000123

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: processed material
subclass of: OBI_1110108
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
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.
editor preferred term: cloning vector
has curation status: IAO_0000123

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
term editor: Kevin Clancy, Bjoern Peters
editor preferred term: restriction enzyme based cloning
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.
has curation status: IAO_0000123

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
term editor: James Malone
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.
editor preferred term: Student's t-test
definition source: WEB: http://en.wikipedia.org/wiki/T-test
has curation status: IAO_0000123

material sample role
type: Class
subclass of: specimen role
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.
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
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.
editor preferred term: material sample role
has curation status: IAO_0000125

topologically preserved clustered data set
type: Class
subclass of: clustered data set
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
example of usage: the output data set generated from a self-organizing map.
editor preferred term: topologically preserved clustered data set
has curation status: IAO_0000125

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
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
editor preferred term: nucleic acid restriction enzyme digest
has curation status: IAO_0000123

immune response assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: immune response
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: assay objective
subclass of: assay
definition: an assay with the objective to determine information about an immune response
editor preferred term: immune response assay
has curation status: IAO_0000123

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
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
editor preferred term: material sampling process
has curation status: IAO_0000123

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: OBI_0100051
definition: A material entity that has the material sample role
term editor: OBI: workshop
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.
editor preferred term: material sample
ISA alternative term: sample
alternative term: sample population
has curation status: IAO_0000123

bisulfite sequencing
type: Class
subclass of: DNA sequencing
subclass of: DNA methylation profiling by high throughput sequencing assay
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: deoxyribonucleic acid
    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: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: DNA residue methylation
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: DNA sequence data
    intersection of: Restriction
      on property: is about
      some values from: regulation of DNA methylation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: epigenetic modification identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: hydrogensulfite
subclass of: Restriction
  on property: has part
  some values from: DNA sequencing
editor note: 8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing.
definition: An assay which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
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. Genome Res. 2009 Jul 6.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia
editor preferred term: bisulfite sequencing
has curation status: IAO_0000120

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
alternative term: classification and regression trees
definition: A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
definition source: BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
editor preferred term: CART
term editor: James Malone
has curation status: IAO_0000122

study design independent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: OBI_0500000
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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
ISA alternative term: study factor
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.
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
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
alternative term: independent variable
alternative term: experimental factor
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 preferred term: study design independent variable
has curation status: IAO_0000122

study design dependent variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: OBI_0500000
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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
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.
alternative term: dependent variable
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
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.
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 preferred term: study design dependent variable
has curation status: IAO_0000122

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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A 'blue top' test tube that contains anticoagulant for storing blood specimens'
term editor: Person:Alan Ruttenberg
editor preferred term: anticoagulant-containing test tube
has curation status: IAO_0000120

study design controlled variable
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: part of
  some values from: OBI_0500000
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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/Control_variable
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling
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.
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
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.
alternative term: controlled variable
editor preferred term: study design controlled variable
has curation status: IAO_0000122

human antithrombin-III (AT-III) in blood assay
type: Class
subclass of: analyte assay
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: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: analyte measurement objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
definition: An assay to measure the amount of antithrombin III in blood.
example of usage: PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
term editor: Person:Alan Ruttenberg
definition source: WEB:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06
editor preferred term: human antithrombin-III (AT-III) in blood assay
has curation status: IAO_0000122

fluorescently labeled MHC multimer
type: Class
subclass of: OBI_0001936
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600038
subclass of: Restriction
  on property: has part
  some values from: REO_0000280
subclass of: Restriction
  on property: bearer of
  some values from: PATO_0000018
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
editor preferred term: fluorescently labeled MHC multimer
has curation status: IAO_0000123

survival rate
type: Class
subclass of: measurement datum
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
editor preferred term: survival rate
has curation status: IAO_0000120

recombinant BAC cloning
type: Class
subclass of: OBI_0600064
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
editor preferred term: recombinant BAC cloning
has curation status: IAO_0000123

multiple testing correction objective
type: Class
subclass of: OBI_0200186
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
example of usage: Application of the Bonferroni correction
definition source: http://en.wikipedia.org/wiki/Multiple_Testing_Correction
alternative term: multiple comparison correction objective
editor preferred term: multiple testing correction objective
has curation status: IAO_0000120

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200188
subclass of: OBI_0200171
definition: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
term editor: Helen Parkinson
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
definition source: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29
editor preferred term: statistical model validation
has curation status: IAO_0000120

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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
editor preferred term: double blind study execution
definition source: http://clinicaltrials.gov/ct2/info/glossary#double
has curation status: IAO_0000120

transcription factor binding site
type: Class
subclass of: sequence feature annotation
comment: PLace_holder for sequence ontology term
definition source: SO:0000235
editor preferred term: transcription factor binding site
has curation status: IAO_0000002

glucometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A measurement device with the function to measure and record the level/amount of glucose in a blood sample
example of usage: Diabetic patients use glucometers to determine their glucose levels
term editor: PERSON:Frank Gibson
term editor: PERSON:Helen Parkinson
editor preferred term: glucometer
alternative term: glucose meter
definition source: http://en.wikipedia.org/wiki/Glucose_meter
has curation status: IAO_0000122

purification objective
type: Class
subclass of: separation into different composition objective
curator note: 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
definition source: BP
term editor: PERSON:Bjoern Peters
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
alternative term: isolation 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

obsolete_primary structure of protein
type: Class
subclass of: ObsoleteClass
term editor: Person:Bjoern Peters
example of usage: SIINFEKL' is the primary structure of a peptide
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
editor preferred term: obsolete_primary structure of protein
comment: replaced by SO_0000104 polypeptide
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

capsule shell
type: Class
subclass of: material entity
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
definition: a small rounded gelatinous container
editor preferred term: capsule shell
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
has curation status: IAO_0000120

recombinant phage cloning
type: Class
subclass of: OBI_0600064
term editor: Helen Parkinson
example of usage: Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
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.
definition source: http://www.ncbi.nlm.nih.gov/books/bv.fcgi
editor preferred term: recombinant phage cloning
has curation status: IAO_0000120

cross linking
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: molecular entity
definition: A process in which bonds are created that link one polymer to another
term editor: PERSON: Chris Stoeckert
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
definition source: http://en.wikipedia.org/wiki/Cross-link
has curation status: IAO_0000120

spike train datum
type: Class
subclass of: measurement datum
definition: A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
term editor: Helen Parkinson, Alan Ruttenberg
definition source: Jessica Turner, NIF
example of usage: Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
editor note: needs more work to see exactly what the data set looks like - HP
editor preferred term: spike train datum
alternative term: spike train measurement
has curation status: IAO_0000120

prothrombin time assay
type: Class
subclass of: assay
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: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
example of usage: PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
term editor: Person:Alan Ruttenberg
definition: The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma.
definition source: WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06
editor preferred term: prothrombin time assay
has curation status: IAO_0000120

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
example of usage: Denaturing DNA in alcohol
definition: Is a process in which the tertiary or secondary structure of a polymer is disrupted
editor preferred term: denaturing
definition source: http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
has curation status: IAO_0000123

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: bearer of
        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 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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
term editor: Person:Alan Ruttenberg
editor preferred term: informing investigator of subject study arm
has curation status: IAO_0000120

antithrombin-III (AT-III) berichrome assay
type: Class
subclass of: human antithrombin-III (AT-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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
definition source: WEB:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
editor preferred term: antithrombin-III (AT-III) berichrome assay
editor note: todo Reagents from Berichrom(r) Antithrombin III (A) and standard human plasma
has curation status: IAO_0000120

material maintenance objective
type: Class
subclass of: objective specification
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
editor preferred term: material maintenance objective
definition source: PERSON: Bjoern Peters
has curation status: IAO_0000122

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
definition source: Helen Parkinson, Jessica Turner, Dirk Derom
term editor: Helen Parkinson, Jessica Turner, Dirk Derom
example of usage: The presentation of a flashing light to a monkey during reward training
definition: a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
editor preferred term: presentation of stimulus
alternative term: stimulation of organism
has curation status: IAO_0000120

spectrolyse heparin antifactor-Xa assay
type: Class
subclass of: assay
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: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
definition: A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma. The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, 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.
example of usage: PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
term editor: Person:Alan Ruttenberg
definition source: WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06
editor preferred term: spectrolyse heparin antifactor-Xa assay
has curation status: IAO_0000120

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
definition source: Alan Ruttenberg
example of usage: Amplied DNA created by PCR
definition: DNA that has been produced in an enzymatic amplification process
term editor: PERSON: Alan Ruttenberg
editor preferred term: amplified DNA
has curation status: IAO_0000122

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
subclass of: Restriction
  on property: has_specified_input
  some values from: Homo sapiens
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.
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
term editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
editor preferred term: informed consent process
has curation status: IAO_0000122

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: SO_0000001
term editor: BP et al
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
editor preferred term: primary structure of DNA macromolecule
has curation status: IAO_0000123

measuring neural activity in the caudate nucleus
type: Class
subclass of: extracellular electrophysiology recording
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: measure function
    intersection of: Restriction
      on property: inheres in
      some values from: micro electrode
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001873
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
term editor: Helen Parkinson
definition source: Jessica Turner, NIF, Dirk Derom, OBI
definition: The process of measuring neural activity in the caudate nucleus
editor preferred term: measuring neural activity in the caudate nucleus
has curation status: IAO_0000120

to be treated with active ingredient role
type: Class
subclass of: participant under investigation role
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
definition source: PERSON: Helen Parkinson
term editor: Person:Alan Ruttenberg
example of usage: Role of a patient in a group treated with an active substance in a clinical trial
editor preferred term: to be treated with active ingredient role
has curation status: IAO_0000122

guar gum
type: Class
subclass of: material entity
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
editor preferred term: guar gum
definition source: http://en.wikipedia.org/wiki/Guar_gum
has curation status: IAO_0000120

Berichrom(r) Antithrombin III (A) Kit
type: Class
subclass of: processed material
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor preferred term: Berichrom(r) Antithrombin III (A) Kit
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
has curation status: IAO_0000120

micro electrode
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: is_manufactured_by
  some values from: organization
subclass of: Restriction
  on property: has function
  some values from: measure function
example of usage: A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
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
definition source: Jessica Turner, Dirk Derom
editor preferred term: micro electrode
alternative term: micro electrode measuring device
has curation status: IAO_0000120

fucoidan
type: Class
subclass of: molecular entity
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
editor preferred term: fucoidan
definition source: http://en.wikipedia.org/wiki/Fucoidan
has curation status: IAO_0000120

calibration
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement device
subclass of: Restriction
  on property: has part
  some values from: assay
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
editor preferred term: calibration
example of usage: the process of using pH buffer adjust a pH meter
has curation status: IAO_0000122

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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
definition: Storage of a blood specimen in a tube with anticoagulant
editor preferred term: anticoagulant tube storage of blood specimen
has curation status: IAO_0000120

activated partial thromboplastin time (aPTT) assay
type: Class
subclass of: assay
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: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
definition: An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms.
example of usage: PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent.
term editor: Person:Alan Ruttenberg
definition source: WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06
editor preferred term: activated partial thromboplastin time (aPTT) assay
has curation status: IAO_0000120

filled capsule
type: Class
subclass of: pill
subclass of: Restriction
  on property: has part
  some values from: capsule shell
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A pill in the form of a small rounded gelatinous container with medicine inside.
term editor: Person:Alan Ruttenberg
editor preferred term: filled capsule
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
has curation status: IAO_0000120

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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
editor preferred term: single blind study execution
has curation status: IAO_0000120

thrombin time assay
type: Class
subclass of: assay
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: scalar measurement datum
      intersection of: Restriction
        on property: is about
        some values from: blood coagulation
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
definition: A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time
example of usage: PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
term editor: Person:Alan Ruttenberg
definition source: WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06
editor preferred term: thrombin time assay
has curation status: IAO_0000120

recombinant YAC cloning
type: Class
subclass of: OBI_0600064
term editor: Helen Parkinson
example of usage: Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
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
definition source: http://www.ncbi.nlm.nih.gov/books/bv.fcgi
editor preferred term: recombinant YAC cloning
has curation status: IAO_0000123

to be treated with placebo role
type: Class
subclass of: participant under investigation role
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
editor preferred term: to be treated with placebo role
has curation status: IAO_0000120

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 note: 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A planned process, part of a study design execution, during which the treatment of subjects is ongoing
term editor: Person:Alan Ruttenberg
editor preferred term: treatment portion of study execution
has curation status: IAO_0000120

pill
type: Class
subclass of: processed material
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
editor preferred term: pill
has curation status: IAO_0000120

research organization
type: Class
subclass of: organization
definition: An organization formed with a goal to have its members conduct investigations
term editor: Person:Bjoern Peters
example of usage: The SALK institute is a research organization.
editor preferred term: research organization
has curation status: IAO_0000123

obsolete_primary structure of sequence macromolecule
type: Class
subclass of: ObsoleteClass
editor note: 2010-06-28 Alan Ruttenberg. This term and its children to be replaced by sequence ontology terms once we figure out what the right terms are .
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
editor note: These are all placeholders and should be replaced by SO terms
editor preferred term: obsolete_primary structure of sequence macromolecule
comment: replaced by SO_0000001 region
curator note: these are not in great shape yet; need to clarify how what a 'sequence macromolecule is' and how it differes from molecules in general (directivity of certain bonds, linear connectivity along that type of bond etc.)
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

DNA residue methylation
type: Class
subclass of: PATO_0001237
editor preferred term: DNA residue methylation
definition: a quality of a DNA residue that has a methyl group attached to it
has curation status: IAO_0000123

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
definition: A device in which a measure function inheres.
example of usage: A ruler, a microarray scanner, a Geiger counter.
term editor: GROUP:OBI Philly workshop
definition source: OBI
editor preferred term: measurement device
has curation status: IAO_0000122

high molecular weight DNA extract
type: Class
subclass of: DNA extract
example of usage: Extraction of chromosomal DNA from mammalian cells by first isolating nucei
definition source: OBI
term editor: PERSON:Chris Stoeckert
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.
editor preferred term: high molecular weight DNA extract
has curation status: IAO_0000120

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
definition: A person or organization that has a manufacturer role
editor preferred term: manufacturer
has curation status: IAO_0000123

test tube
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
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 term: collection tube
definition source: http://en.wikipedia.org/wiki/Test_tube
alternative term: sample tube
editor preferred term: test tube
has curation status: IAO_0000120

oral ingestion of pill
type: Class
equivalent class: Class
  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: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0000165
  intersection of: Restriction
    on property: has_specified_input
    some values from: pill
subclass of: oral administration
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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
editor preferred term: oral ingestion of pill
has curation status: IAO_0000120

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
editor preferred term: material maintenance
has curation status: IAO_0000123

labeled oligonucleotide
type: Class
subclass of: OBI_0001936
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600038
subclass of: Restriction
  on property: has part
  some values from: REO_0000280
editor note: 2010-01-31: Philippe Rocca-Serra placeholder
term editor: Person: Philippe Rocca-Serra
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 preferred term: labeled oligonucleotide
has curation status: IAO_0000123

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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
definition: 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
editor preferred term: unblinding process
has curation status: IAO_0000120

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 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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A process in which a subject receives an informed consent document and agrees that they have understood it
term editor: Person:Alan Ruttenberg
editor preferred term: subject agrees they understand informed consent document
has curation status: IAO_0000120

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 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
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
term editor: Person:Alan Ruttenberg
editor preferred term: informing subject of study arm
has curation status: IAO_0000120

Sysmex CA-6000 Coagulation Analyzer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: is_manufactured_by
  has value: OBI_0000829
subclass of: Restriction
  on property: has function
  some values from: measure function
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
editor preferred term: Sysmex CA-6000 Coagulation Analyzer
definition: The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
definition source: web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
has curation status: IAO_0000120

hospital
type: Class
subclass of: organization
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A medical organization at which sick or injured people are given clinical care
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
editor preferred term: hospital
definition source: http://www.golovchenko.org/cgi-bin/wnsearch#2n
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]
definition source: modified from the wording of the wordnet definition
has curation status: IAO_0000120

primary structure of RNA molecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: ribonucleic acid
subclass of: SO_0000001
term editor: Person:Bjoern Peters
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
editor preferred term: primary structure of RNA molecule
has curation status: IAO_0000123

test substance role
type: Class
subclass of: role
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
definition source: Group:OBI
term editor: Person:Alan Ruttenberg
example of usage: fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
editor preferred term: test substance role
has curation status: IAO_0000120

polyA RNA extraction
type: Class
subclass of: OBI_0666666
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
editor preferred term: polyA RNA extraction
has curation status: IAO_0000120

organellar RNA extraction
type: Class
subclass of: OBI_0666666
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
editor preferred term: organellar RNA extraction
has curation status: IAO_0000120

obsolete_diethyl pyrocarbonate
type: Class
subclass of: ObsoleteClass
comment: Replaced by CHEBI_59051 Diethylpyrocarbonate
editor preferred term: obsolete_diethyl pyrocarbonate
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

record of missing knowledge
type: Class
subclass of: information content entity
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.
term editor: Bjoern Peters
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.
definition: a information content entity created to indicate that information about something is not available to the person recording it.
editor preferred term: record of missing knowledge
has curation status: IAO_0000120

western blot analysis
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: inheres in
        some values from: peptide
  intersection of: Restriction
    on property: has_specified_input
    some values from: peptide
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: Philippe Rocca-Serra, IEDB
definition source: Philippe Rocca-Serra, IEDB
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.
editor preferred term: western blot analysis
has curation status: IAO_0000120

total RNA extraction
type: Class
subclass of: OBI_0666666
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
editor preferred term: total RNA extraction
has curation status: IAO_0000120

obsolete intracellular material detection by flow cytometry assay
type: Class
subclass of: ObsoleteClass
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.
IEDB alternative term: intracellular staining
editor preferred term: obsolete intracellular material detection by flow cytometry assay
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000227
term replaced by: flow cytometry assay

complementary nucleotide probe role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: nucleic acid
example of usage: A primer in a PCR reaction. A probe on an Affymetrix chip.
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
editor preferred term: complementary nucleotide probe role
has curation status: IAO_0000120

record of unknown sex
type: Class
subclass of: record of missing knowledge
subclass of: Restriction
  on property: is about
  some values from: PATO_0000047
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.
term editor: Bjoern Peters
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.
definition: a record indicating that the biological sex of an organism is not known.
editor preferred term: record of unknown sex
has curation status: IAO_0000120

cytoplasmic RNA extraction
type: Class
subclass of: OBI_0666666
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
editor preferred term: cytoplasmic RNA extraction
has curation status: IAO_0000120

northern blot analysis
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: complementary nucleotide probe role
    intersection of: Restriction
      on property: inheres in
      some values from: nucleic acid
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: inheres in
      some values from: polyA RNA extract
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
editor note: 2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information
example of usage: PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K.
term editor: Person: Philippe Rocca-Serra
definition: a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager
alternative term: northern blot
editor preferred term: northern blot analysis
has curation status: IAO_0000123

Likelihood-ratio test
type: Class
subclass of: OBI_0200000
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.
editor preferred term: Likelihood-ratio test
term editor: Tina Boussard
has curation status: IAO_0000123

nuclear RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: nuclear RNA extraction
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.
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)
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: nuclear RNA extract
has curation status: IAO_0000120

96-well neutralization assay
type: Class
subclass of: serum neutralization of viral infectivity assay
editor preferred term: 96-well neutralization assay
definition: A serum neutralization of viral infectivity assay which done in a 96-well plate.
curator note: MC: 20100217: microneutralization is used by the influenza community, to refer to a nutralizationassay at a smaller scale. However smaller is difficult to define accurately, and we therefore chose a label being more specific.
alternative term: microneutralization assay
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
has curation status: IAO_0000120

establishing cancer cell line
type: Class
subclass of: OBI_0001867
subclass of: Restriction
  on property: has_specified_output
  some values from: OBI_0001906
example of usage: Establishment of HeLa immortal cell line
comment: Helen Parkinson
editor preferred term: establishing cancer cell line
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
has curation status: IAO_0000123

pattern matching objective
type: Class
subclass of: OBI_0200166
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
editor preferred term: pattern matching objective
has curation status: IAO_0000123

polyA RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: polyA RNA extraction
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
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.)
definition source: UPenn Group
editor preferred term: polyA RNA extract
has curation status: IAO_0000120

single-nucleotide-resolution nucleic acid structure mapping assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: secondary structure of sequence macromolecule
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: assay objective
subclass of: assay
editor note: 2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy.
term editor: Person: Philippe Rocca-Serra
definition source: RNAO
definition: is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay
has curation status: IAO_0000120

viral hemagglutination assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: Restriction
  on property: has part
  some values from: induced hemagglutination
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Viruses
alternative term: HA
alternative term: HI
definition: The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination.
definition source: WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
editor preferred term: viral hemagglutination assay
alternative term: viral hemeagglutination assay
has curation status: IAO_0000120

serum neutralization of viral infectivity assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
definition: A quantitative assay where 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 simple process of dilution provides a way to compare the virus- neutralizing abilities of different sera. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked.
curator note: MC, 20100217: I added influenza neutralization assay as alternative term. This should be tagged with a community specific value, eg "influenza ontology" or else.
definition source: WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/
alternative term: influenza neutralization assay
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
editor preferred term: serum neutralization of viral infectivity assay
has curation status: IAO_0000120

pre-mortem specimen
type: Class
equivalent class: 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
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: specimen with pre- or post-mortem status
disjoint with: post mortem specimen
term editor: Bjoern Peters
definition: a specimen that was taken from a live organism
example of usage: material obtained through a liver biopsy from a human patient
editor preferred term: pre-mortem specimen
definition source: MO_705 premortem
has curation status: IAO_0000120

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
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
example of usage: Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays.
editor preferred term: detection of specific nucleic acid polymers with complementary probes
has curation status: IAO_0000120

viral hemagglutination inhibition assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_input
    some values from: Viruses
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: induced hemagglutination
subclass of: assay
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 hemagglutination inhibition by the antibody.
definition source: Bjoern and Melanie
term editor: Bjoern and Melanie
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.
editor preferred term: viral hemagglutination inhibition assay
has curation status: IAO_0000120

cytoplasmic RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: cytoplasmic RNA extraction
definition: A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
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.)
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: cytoplasmic RNA extract
has curation status: IAO_0000120

cell line immortalization
type: Class
subclass of: OBI_0001867
subclass of: Restriction
  on property: has_specified_output
  some values from: immortal cell line
subclass of: Restriction
  on property: has part
  some values from: OBI_0001907
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.
term editor: Bjoern Peters
definition source: OBI
example of usage: Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
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 preferred term: cell line immortalization
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.
alternative term: 'establishing immortal cell line through directed genetic modification'
has curation status: IAO_0000123

random primed DNA labeling
type: Class
subclass of: OBI_0600038
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.
example of usage: PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9.
term editor: Person: Bjoern Peters Person: Chris Stoeckert
term editor: Person: Philippe Rocca-Serra
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
editor preferred term: random primed DNA labeling
has curation status: IAO_0000120

RNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0666666
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acid
definition source: Group: UPenn Group
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
editor preferred term: RNA extract
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
has curation status: IAO_0000120

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
definition: A cytometry assay that monitors a cell population to track how many are killed by other cells.
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.
definition source: IEDB
term editor: IEDB
editor preferred term: cell-cell killing assay
has curation status: IAO_0000120

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: OBI_0100026
subclass of: cell-cell killing assay
definition: A cell killing assay that measures if and how many target cells are killed within an organism.
definition source: IEDB
term editor: IEDB
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.
editor preferred term: in vivo cell killing assay
has curation status: IAO_0000120

secondary structure of sequence macromolecule
type: Class
subclass of: PATO_0001237
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
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.
term editor: Person: Philippe Rocca-Serra
definition source: Wikipedia
editor preferred term: secondary structure of sequence macromolecule
has curation status: IAO_0000002

nuclear RNA extraction
type: Class
subclass of: OBI_0666666
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
editor preferred term: nuclear RNA extraction
has curation status: IAO_0000120

survival curve
type: Class
subclass of: line graph
subclass of: Restriction
  on property: is about
  some values from: survival rate
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
editor preferred term: survival curve
has curation status: IAO_0000122

cell proliferation 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: evaluant role
        intersection of: Restriction
    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 proliferation
subclass of: OBI_0001977
definition: A cytometry assay which measures the degreee to which input cells are replicating.
term editor: IEDB
definition source: IEDB
example of usage: Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
editor preferred term: cell proliferation assay
has curation status: IAO_0000120

Southern blot analysis
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: complementary nucleotide probe role
    intersection of: Restriction
      on property: inheres in
      some values from: nucleic acid
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: evaluant role
    intersection of: Restriction
      on property: inheres in
      some values from: high molecular weight DNA extract
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: site
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        intersection of: scattered molecular aggregate
        intersection of: Restriction
editor note: 2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe'
editor note: 2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern.
definition source: OBI & Wikipedia
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. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
term editor: Person: Philippe Rocca-Serra
alternative term: Southern blot
editor preferred term: Southern blot analysis
definition: Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
has curation status: IAO_0000120

real time polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: polymerase chain reaction
definition: A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify 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.
alternative term: Q-PCR
definition source: WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
alternative term: kinetic polymerase chain reaction
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
alternative term: qPCR
alternative term: quantitative real time polymerase chain reaction
ISA alternative term: real time PCR
editor preferred term: real time polymerase chain reaction assay
has curation status: IAO_0000120

protein extract
type: Class
subclass of: extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302884
subclass of: Restriction
  on property: has part
  some values from: PR_000000001
definition source: OBI & wikipedia
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.
term editor: Person: Philippe Rocca-Serra
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,
editor preferred term: protein extract
has curation status: IAO_0000120

total RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: total RNA extraction
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.
example of usage: Extraction of total RNA from cells with Qiagen mini RNeasy kit.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: total RNA extract
has curation status: IAO_0000120

secondary structure of RNA molecule
type: Class
subclass of: secondary structure of sequence macromolecule
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
example of usage: PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
term editor: Person: Philippe Rocca-Serra
editor preferred term: secondary structure of RNA molecule
has curation status: IAO_0000123

DEPC structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: diethyl pyrocarbonate
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
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.
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
has curation status: IAO_0000122

organellar RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: organellar RNA extraction
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.
example of usage: Extraction of organellar RNA from plant cells using organellar RNA binding protein.
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
editor preferred term: organellar RNA extract
has curation status: IAO_0000120

post mortem specimen
type: Class
equivalent class: 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
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: specimen with pre- or post-mortem status
term editor: Bjoern Peters
definition: a specimen that was taken from a dead organism
editor preferred term: post mortem specimen
example of usage: the spleen taken from a dead mouse
definition source: MO_416 postmortem
has curation status: IAO_0000120

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: OBI_0100060
subclass of: cell-cell killing assay
definition: A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
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.
term editor: IEDB
definition source: IEDB
editor preferred term: in vitro cell killing assay
has curation status: IAO_0000120

reporter cell line analyte detection bioassay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: has part
  some values from: OBI_0600024
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: inheres in
        some values from: cell line
  intersection of: Restriction
    on property: has_specified_input
    some values from: cell line
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.
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.
definition source: IEDB
term editor: IEDB
editor preferred term: reporter cell line analyte detection bioassay
has curation status: IAO_0000120

sequence feature annotation
type: Class
subclass of: information content entity
definition source: Bjoern Peters
term editor: Bjoern Peters
definition: Information about a sequence region
comment: place holder for sequence ontology term
editor preferred term: sequence feature annotation
has curation status: IAO_0000120

induced hemagglutination
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: erythrocyte
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'.
definition: The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
definition source: WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination
alternative term: hemeagglutination
editor preferred term: induced hemagglutination
term editor: person: Bjoern Peters
term editor: person: Melanie Courtot
has curation status: IAO_0000120

supplying
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
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.
example of usage: Jackson Labs supplies mouse strains.
term editor: Jennifer Fostel
definition source: Jennifer Fostel
definition: The planned process of providing material entities to be used in an investigation.
editor preferred term: supplying
has curation status: IAO_0000120

labeled DNA extract
type: Class
subclass of: labeled nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
subclass of: Class
  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 role
    some values from: specimen role
term editor: Group: OBI group
definition source: Group: OBI group
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
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 preferred term: labeled DNA extract
has curation status: IAO_0000120

cloacal specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has role
  some values from: specimen role
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
editor preferred term: cloacal specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120

radio immuno assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: radioactivity detection
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: REO_0000171
      intersection of: Restriction
        on property: inheres in
        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: bearer of
        some values from: PATO_0001741
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.
definition source: IEDB
term editor: IEDB
example of usage: To evaluate the specificity of antibody binding to 35S-labeled IA-2(256ÛÒ760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256ÛÒ760) fragments were tested. Unlabeled recombinant IA-2(256ÛÒ760) 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 4å¡C with patient sera. The following day, after incubation with radiolabeled 35SÛÒIA-2(256ÛÒ760) or 35SÛÒIA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
editor preferred term: radio immuno assay
has curation status: IAO_0000120

real time reverse-transcription polymerase chain reaction assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: real time polymerase chain reaction assay
      intersection of: Restriction
        on property: immediately preceded by
        some values from: OBI_0600028
  intersection of: Restriction
    on property: immediately preceded by
    some values from: OBI_0600028
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: gene expression
definition: Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: RRT-PCR
alternative term: RT-rt PCR
alternative term: qRT-PCR
editor preferred term: real time reverse-transcription polymerase chain reaction assay
has curation status: IAO_0000120

X-ray crystallography assay
type: Class
subclass of: OBI_0600045
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: X-ray source
  intersection of: Restriction
    on property: has_specified_input
    some values from: X-ray source
definition: A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
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.
definition source: IEDB
term editor: IEDB
editor preferred term: X-ray crystallography assay
has curation status: IAO_0000120

promoter activity detection by reporter gene assay
type: Class
subclass of: binding 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 binding
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.
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.
definition source: IEDB
term editor: IEDB
editor preferred term: promoter activity detection by reporter gene assay
has curation status: IAO_0000120

nasopharyngeal aspirate specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has role
  some values from: specimen role
definition: A speciemn 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
editor preferred term: nasopharyngeal aspirate specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120

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 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.
definition: A storage process in temperature that maintenance the frozen status of the stored entities.
definition source: OBI
term editor: Person: Alan Ruttenberg, Mathias Brochhausen
example of usage: a fozen pellet used for later assay
editor preferred term: freezing storage
definition source: MO_481 frozen_storage
has curation status: IAO_0000120

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: fluorescence detection assay
subclass of: OBI_0001977
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
definition source: IEDB
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.
editor preferred term: flow cytometry assay
has curation status: IAO_0000120

nasal swab specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has role
  some values from: specimen role
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
editor preferred term: nasal swab specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: IAO_0000120

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
definition: A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
alternative term: D-MEM
alternative term: DMEM
editor preferred term: Dulbecco's modified Eagle medium
editor note: Logical definition should contain all components listed in textual definition at some point.
term editor: PERSON:Bjoern Peters
has curation status: IAO_0000123

animal euthanization
type: Class
subclass of: OBI_0600006
subclass of: Restriction
  on property: has_specified_input
  some values from: Vertebrata <Metazoa>
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
definition source: Melissa Haendel
example of usage: Rats were euthanized with CO2
editor preferred term: animal euthanization
alternative term: animal sacrifice
comment: may later be refined with more specific list of organisms
has curation status: IAO_0000120

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: fluorescence detection assay
subclass of: analyte assay
definition: An analyte assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes.
term editor: IEDB
definition source: IEDB
alternative term: Luminex assay
example of usage: Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture.
editor preferred term: cytometric bead array assay
has curation status: IAO_0000120

labeled RNA extract
type: Class
subclass of: labeled nucleic acid extract
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acid
subclass of: Class
  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 role
    some values from: specimen role
term editor: Group: OBI group
definition source: Group: OBI group
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
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 preferred term: labeled RNA extract
has curation status: IAO_0000120

frozen specimen
type: Class
equivalent class: Class
  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
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
disjoint with: paraffin specimen
disjoint with: lyophilized specimen
disjoint with: fresh specimen
disjoint with: agar stab specimen
definition: A specimen that has been frozen in order to store it.
example of usage: Frozen blood plasma
definition source: MO_610 frozen_sample
term editor: Person:Alan Ruttenberg
editor preferred term: frozen specimen
has curation status: IAO_0000123

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: inheres in
        some values from: surface plasmon resonance instrument
  intersection of: Restriction
    on property: has_specified_input
    some values from: surface plasmon resonance instrument
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.
definition source: IEDB
term editor: IEDB
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.
editor preferred term: surface plasmon resonance binding assay
has curation status: IAO_0000120

labeled specimen
type: Class
equivalent class: Class
  intersection of: OBI_0100051
  intersection of: Restriction
    on property: has part
    some values from: REO_0000280
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600038
subclass of: processed specimen
subclass of: OBI_0001936
definition: A specimen that has been modified in order to be able to detect it in future experiments
term editor: OBI group
editor note: added during call 3/1/2010
editor preferred term: labeled specimen
has curation status: IAO_0000123

infectious agent
type: Class
equivalent class: Restriction
  on property: bearer of
  some values from: OBI_1110093
subclass of: OBI_0100026
term editor: IEDB
definition source: IEDB
editor preferred term: infectious agent
definition: is a material entity bearing the disposition to infect an organism
has curation status: IAO_0000123

obsolete_ambidexterious handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_ambidexterious handedness
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

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
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a storage process with input material entity and output freeze dried material for long time storage
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
editor preferred term: lyophilization storage
has curation status: IAO_0000123

material combination function
type: Class
subclass of: function
definition: A material separation function is a function that decreases the resolution between two or more material entities.
example of usage: A stirrer has a material combination function
term editor: Helen Parkinson
definition source: OBI
editor preferred term: material combination function
has curation status: IAO_0000120

obsolete_training service provider role
type: Class
subclass of: ObsoleteClass
example of usage: EBI provides training on databases and tools and has a training service provider role
definition source: OBI
term editor: PERSON:Helen Parkinson
definition: a service provider role which is realized by a servicer provider organization performing some training
editor note: obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
editor preferred term: obsolete_training service provider role
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

calorimeter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
term editor: PERSON:Bjoern Peters
editor preferred term: calorimeter
alternative term: calorimetry instrument?
definition source: http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm
has curation status: IAO_0000120

study intervention
type: Class
subclass of: planned process
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
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
definition source: GROUP: OBI
term editor: PERSON: Bjoern Peters
editor preferred term: study intervention
definition: the part of the execution of an intervention design study which is varied between two or more subjects in the study
has curation status: IAO_0000120

material separation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: material separation function
subclass of: device
definition: A device with a separation function realized in a planed process
example of usage: flow cytometer
editor preferred term: material separation device
has curation status: IAO_0000123

positron emission tomography scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
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 term: PET scanner?
definition source: http://en.wikipedia.org/wiki/Positron_emission_tomography
editor preferred term: positron emission tomography scanner
has curation status: IAO_0000120

intramuscular 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: inheres in
        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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred term: intramuscular injection
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
has curation status: IAO_0000123

micromanipulator
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: micromanipulator
has curation status: IAO_0000120

obsolete_material access provider role
type: Class
subclass of: ObsoleteClass
example of usage: A person or organization who provides access to a DNA sequencer.
definition source: OBI
term editor: PERSON:Helen Parkinson
definition: a service provider role which is realized by a servicer provider organization performing access to some material
editor note: obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
editor preferred term: obsolete_material access provider role
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

obsolete_left handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_left handedness
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: OBI_0001930
definition: A measurement datum that is reported on a categorical scale
term editor: Bjoern Peters
definition source: Bjoern Peters
editor preferred term: categorical measurement datum
alternative term: nominal mesurement datum
has curation status: IAO_0000120

training process
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: training objective
subclass of: planned process
definition: a process that achieves a training objective
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
editor preferred term: training process
has curation status: IAO_0000123

optical microscope
type: Class
subclass of: OBI_0400169
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
editor preferred term: optical microscope
has curation status: IAO_0000120

service consumer role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
example of usage: A biologist who uses a sequencing services fulfills the role of a service consumer
definition source: OBI
term editor: Person:Helen Parkinson
definition: a role which inheres in a person who uses a service
editor preferred term: service consumer role
has curation status: IAO_0000120

intradermal 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: inheres in
        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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
editor preferred term: intradermal injection
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
has curation status: IAO_0000123

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
term editor: PERSON:Philippe Rocca-Serra
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.
definition source: RNA ontology group
editor preferred term: chemical cleavage
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
has curation status: IAO_0000120

handedness assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: PATO_0002201
subclass of: assay
definition: A handedness assay 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
example of usage: The Edinburgh handedness assay is a specific method of determing handedness
editor preferred term: handedness assay
alternative term: handedness test
definition source: http://en.wikipedia.org/wiki/Handedness
has curation status: IAO_0000120

vibration isolation table
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: environment control function
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
editor preferred term: vibration isolation table
has curation status: IAO_0000120

sterilization function
type: Class
subclass of: function
definition: a function to remove viable organisms from an input material
editor preferred term: sterilization function
has curation status: IAO_0000123

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: planned process
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
term editor: PERSON:Helen Parkinson
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
editor preferred term: service provider role
has curation status: IAO_0000123

oscilloscope
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: oscilloscope
has curation status: IAO_0000120

accessed material role
type: Class
subclass of: role
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
editor preferred term: accessed material role
definition: is realized in a planned process where the bearer participates
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

paraffin specimen
type: Class
equivalent class: Class
  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
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
disjoint with: lyophilized specimen
disjoint with: fresh specimen
disjoint with: agar stab specimen
definition source: MO_990 paraffin_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
example of usage: liver tissue embedded in paraffin
editor preferred term: paraffin specimen
has curation status: IAO_0000123

compound treatment 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: Class
subclass of: intervention design
definition source: MO_555 compound_treatment_design
term editor: PERSON: Bjoern Peters
editor note: This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
definition: an intervention design in which the treatment is the administration of a compound
editor preferred term: compound treatment design
has curation status: IAO_0000120

oral administration
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: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0000165
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
definition: The administration of a substance into the mouth of an organism
editor preferred term: oral administration
has curation status: IAO_0000123

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: OBI_0100051
subclass of: processed material
subclass of: OBI_0100051
definition: A specimen that has been intentionally physically modified.
definition source: Bjoern Peters
term editor: Bjoern Peters
editor preferred term: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
comment: A tissue sample that has been sliced and stained for a histology study.
has curation status: IAO_0000122

subcutaneous 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: inheres in
        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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
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
editor preferred term: subcutaneous injection
has curation status: IAO_0000123

electrode puller
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: electrode puller
definition source: http://faculty.plattsburgh.edu/donald.slish/Puller1.html
has curation status: IAO_0000120

obsolete_handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_handedness
deprecated: true
term replaced by: http://purl.obolibrary.org/obo/PATO_0002201
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

self reported handedness assessment
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: categorical measurement datum
    intersection of: Restriction
      on property: is quality measurement of
      some values from: PATO_0002201
definition: An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories.
editor preferred term: self reported handedness assessment
has curation status: IAO_0000123

vibrotome
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: Restriction
    on property: realized in
    all values from: OBI_0600014
subclass of: Restriction
  on property: has function
  some values from: material separation function
definition: A preparation device that uses a vibrating razor blade to cut through tissue.
editor preferred term: vibrotome
has curation status: IAO_0000123

reagent application function
type: Class
subclass of: function
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?
definition: A function that is realized when a reagent is automatically added to some research material.
example of usage: An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
editor preferred term: reagent application function
has curation status: IAO_0000120

addition of molecular tracer function
type: Class
subclass of: reagent application function
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.
example of usage: Immunohistochemical labeling of tissue sections by an autostainer staining system.
term editor: PERSON: Nicole Vasilevsky, Matthew Brush
definition source: PERSON: Nicole Vasilevsky, Matthew Brush
editor preferred term: addition of molecular tracer function
has curation status: IAO_0000120

training objective
type: Class
subclass of: objective specification
example of usage: A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package
definition: An training objective which is fulfilled by the provision of some training
term editor: Helen Parkinson
definition source: OBI
editor preferred term: training objective
has curation status: IAO_0000120

categorical label
type: Class
subclass of: datum label
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
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.
editor preferred term: categorical label
has curation status: IAO_0000120

in live cell assay
type: Class
subclass of: assay
definition: An assay in which a measurement is made by observing entities located in a live cell.
editor preferred term: in live cell assay
has curation status: IAO_0000123

lyophilized specimen
type: Class
equivalent class: Class
  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
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: specimen with known storage state
disjoint with: fresh specimen
disjoint with: agar stab specimen
definition source: MO_589 freeze_dried_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
example of usage: freezing dried DNA
editor preferred term: lyophilized specimen
has curation status: IAO_0000123

in live organism assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has participant
    some values from: Restriction
      on property: located in
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: assay
definition: An assay in which a measurement is made by observing entities located in an organism.
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.
term editor: PERSON:Bjoern Peters
editor preferred term: in live organism assay
alternative term: in vivo assay
has curation status: IAO_0000120

container
type: Class
equivalent class: Restriction
  on property: has function
  some values from: contain function
subclass of: device
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?)
definition: A device that can be used to restrict the location of material entities over time
term editor: PERSON: Bjoern Peters
editor preferred term: container
has curation status: IAO_0000123

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 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…
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
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.
definition source: OBI development call 2012-12-17.
term editor: PERSON: Helen Parkinson
editor preferred term: device
alternative term: instrument
has curation status: IAO_0000122

dose specification
type: Class
subclass of: directive information entity
definition: a directive information entity that describes the dose that will be administered to a target
example of usage: a protocol specifying to administer 1 ml of vaccine to a mouse
editor preferred term: dose specification
has curation status: IAO_0000123

scalar score from composite inputs
type: Class
subclass of: scalar 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
alternative term: questionaire score
editor preferred term: scalar score from composite inputs
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.
curator note: JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation?
definition source: Person: Jessica Turner
term editor: Person: Jessica Turner
has curation status: IAO_0000120

fresh specimen
type: Class
subclass of: specimen with known storage state
disjoint with: agar stab specimen
definition source: MO_730 fresh_sample
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
example of usage: a liver freshly removed from a rat
definition: a specimen that is output of a specimen creation process used for an investigation without storage.
editor preferred term: fresh specimen
has curation status: IAO_0000123

obsolete_electrically powered device
type: Class
subclass of: ObsoleteClass
definition: a processed material created to have a function and which requires electrical power to execute
editor preferred term: obsolete_electrically powered device
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

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
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.
definition source: GROUP: OBI
term editor: Person:Chris Stoeckert
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
editor preferred term: sequence data
has curation status: IAO_0000120

obsolete_right handedness
type: Class
subclass of: ObsoleteClass
editor preferred term: obsolete_right handedness
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000228

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: flow cytometry assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: binding
subclass of: fluorescence detection binding assay
subclass of: OBI_0001977
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
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.
editor preferred term: cell-cell binding detection by flow cytometry assay
has curation status: IAO_0000120

handedness categorical measurement datum
type: Class
subclass of: categorical measurement datum
subclass of: Restriction
  on property: has category label
  some values from: Class
    one of: OBI_0000958
    one of: OBI_0000979
    one of: OBI_0000998
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0002201
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
editor preferred term: handedness categorical measurement datum
has curation status: IAO_0000123

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
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
definition: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
comment: need to specify paraffin or wax is one of specified input of the process
editor preferred term: paraffin storage
has curation status: IAO_0000120

in container assay
type: Class
subclass of: assay
definition: an assay in which a measurement is made by observing entities located in a container.
editor preferred term: in container assay
has curation status: IAO_0000123

obsolete_protocol service provider role
type: Class
subclass of: ObsoleteClass
example of usage: DNA sequencing of a sample by a core lab which returns data to the consumer
term editor: PERSON:Helen Parkinson
definition: a service provider role which is realized by a servicer provider organization performing a protocol execution
editor note: obsolete during the San Diego workshop, March 2011 The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
editor preferred term: obsolete_protocol service provider role
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

agar stab specimen
type: Class
equivalent class: 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
        on property: has role
        some values from: specimen role
subclass of: specimen with known storage state
definition source: MO_971 agar_stab
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
editor preferred term: agar stab specimen
has curation status: IAO_0000123

computed tomography scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
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.
alternative term: CT scanner
term editor: PERSON:Bjoern Peters
alternative term: X-ray computed tomography scanner
editor preferred term: computed tomography scanner
definition source: http://en.wikipedia.org/wiki/X-ray_computed_tomography
has curation status: IAO_0000120

intranasal mucosal administration
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: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: UBERON_0005022
subclass of: OBI_0600007
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
definition: The administration of a substance into the intranasal mucosis of an organism
editor preferred term: intranasal mucosal administration
has curation status: IAO_0000123

dose
type: Class
subclass of: measurement datum
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.
example of usage: An organism has been injected 1ml of vaccine
editor preferred term: dose
has curation status: IAO_0000123

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: growth environment
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
definition: A study design in which the independent variable is the environmental condition in which the specimen is growing
definition source: MO_588 growth_condition_design
term editor: PERSON: Bjoern Peters
editor preferred term: growth condition intervention design
has curation status: IAO_0000120

obsolete_DNA sequencing training service
type: Class
subclass of: ObsoleteClass
editor note: 03/22/2010:workshop: there is a user requirement that not in all cases of the training the trainee gains the skills.
definition: A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
editor preferred term: obsolete_DNA sequencing training service
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

obsolete_general scalar measurement datum
type: Class
subclass of: ObsoleteClass
editor note: 4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3302925&group_id=177891&atid=886178
editor preferred term: obsolete_general scalar measurement datum
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000124

performing a diagnosis
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has_specified_output
  some values from: diagnosis textual entity
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.
definition: The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
editor preferred term: performing a diagnosis
has curation status: IAO_0000123

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 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.
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 preferred term: PCR instrument
has curation status: IAO_0000123

electron microscope
type: Class
subclass of: OBI_0400169
definition: A microscope that produces an image of an object by targeting it with an electron beam
editor preferred term: electron microscope
has curation status: IAO_0000123

Edinburgh score
type: Class
subclass of: scalar score from composite inputs
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Edinburgh handedness assay
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
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
term editor: Person: Alan Ruttenberg
term editor: Person:Jessica Turner
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
definition: A score that measures the dominance of a person's right or left hand in everyday activities.
has curation status: IAO_0000123

DNA sequencing service
type: Class
subclass of: OBI_0001904
subclass of: Restriction
  on property: provides_service_consumer_with
  some values from: DNA sequencing
subclass of: Restriction
  on property: realizes
  some values from: service consumer role
subclass of: Restriction
  on property: realizes
  some values from: service provider role
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 preferred term: DNA sequencing service
editor note: Eagle-i will supply better English definition
has curation status: IAO_0000123

service provision objective
type: Class
subclass of: objective specification
example of usage: A sequencing centre has a service provision objective
definition: An objective which is fulfilled by the provision of some service e.g. a training service
term editor: Helen Parkinson
definition source: OBI
editor preferred term: service provision objective
has curation status: IAO_0000120

intravenous 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: inheres in
        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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
term editor: PERSON: Melanie Courtot
editor preferred term: intravenous injection
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
has curation status: IAO_0000123

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
term editor: Bjoern Peters
definition source: Bjoern Peters
example of usage: Staining cells in a tissue slice with a dye.
definition: The directed combination of a material entity with a specimen.
editor preferred term: administration of material to specimen
has curation status: IAO_0000120

device creation objective
type: Class
subclass of: material transformation objective
definition source: OBI
term editor: PERSON: Helen Parkinson
definition: an objective which aims to create a device with a specified function
editor preferred term: device creation objective
has curation status: IAO_0000120

growth environment
type: Class
subclass of: material entity
definition source: OBI group
term editor: PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
editor note: Right now this may be incomplete. Should also cover e.g. sound, light as well.
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 preferred term: growth environment
has curation status: IAO_0000120

questionnaire
type: Class
subclass of: document
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
editor preferred term: questionnaire
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.
definition source: Merriam-Webster
term editor: PERSON: Jessica Turner
has curation status: IAO_0000120

Edinburgh handedness assay
type: Class
subclass of: handedness assay
subclass of: Restriction
  on property: has_specified_input
  has value: OBI_0001004
subclass of: Restriction
  on property: has_specified_output
  some values from: Edinburgh score
editor preferred term: Edinburgh handedness assay
term editor: PERSON:Jessica Turner
term editor: Person:Alan Ruttenberg
definition: The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, 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.
definition source: WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory
has curation status: IAO_0000120

Faraday cage
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: environment control function
definition: A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
editor preferred term: Faraday cage
alternative term: Faraday shield
term editor: PERSON:Bjoern Peters
definition source: Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
curator note: isolation function? HP
has curation status: IAO_0000120

agar stab storage
type: Class
subclass of: OBI_0302893
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_0100060
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jie Zheng
definition source: UPenn Group
definition: a storage process with input cell culture and agar and output agar stab for long time storage
editor preferred term: agar stab storage
comment: need to specify that agar is one of input for this process
has curation status: IAO_0000120

RNASE CL3 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025478
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:16453415
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE CL3 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse CL3 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse CL3
has curation status: IAO_0000122

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_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
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: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: diethyl pyrocarbonate
editor preferred term: CMCT structure mapping assay
example of usage: PMID:2422386 and PMID:2446263
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
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
alternative term: single nucleotide resolution mapping assay using CMCT probe
has curation status: IAO_0000122

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
definition: A planned process that captures an image of an object.
term editor: PERSON: Jie Zheng
example of usage: Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
alternative term: image acquisition
editor preferred term: image creation
has curation status: IAO_0000123

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: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: EDTA methidiumpropylamide
editor preferred term: MPE-Fe(II) structure mapping assay
example of usage: PMID:6209709
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-MP as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Fe-MP probe
has curation status: IAO_0000122

obsolete_qualitative binding detection assay
type: Class
subclass of: ObsoleteClass
deprecated: true
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
editor preferred term: obsolete_qualitative binding detection assay
has obsolescence reason: IAO_0000103
has curation status: IAO_0000123

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0666667
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
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
editor preferred term: nucleic acid extract
has curation status: IAO_0000120

ENU structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: N-ethyl-N-nitrosourea
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
editor preferred term: ENU structure mapping assay
example of usage: PMID:7002606 and PMID:2446263
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses ENU as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using ENU probe
has curation status: IAO_0000122

RNASE V1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025477
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
example of usage: PMID:7031604
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE V1 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse V1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse V1
has curation status: IAO_0000122

kethoxal structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: 1,1-dihydroxy-3-ethoxy-2-butanone
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: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
definition: is a single-nucleotide-resolution nucleic acid structure mapping assay which uses kethoxal as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
editor preferred term: kethoxal structure mapping assay
example of usage: single nucleotide resolution mapping assay using Kethoxal probe
has curation status: IAO_0000122

single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000000001
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay
term editor: Person: Philippe Rocca-Serra
definition source: RNAO and OBI
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
has curation status: IAO_0000122

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_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
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: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: dimethyl sulfate
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred term: DMS structure mapping assay
example of usage: PMID:6159633 and PMID:2446263
term editor: Person: Philippe Rocca-Serra
definition source: RNA Ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses DMS as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using DMS probe
has curation status: IAO_0000122

DNASE 1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000006592
editor preferred term: DNASE 1 structure mapping assay
alternative term: DNAse footprinting assay
example of usage: PMID:3773731
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
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
alternative term: single nucleotide resolution mapping assay using DNAse I
has curation status: IAO_0000122

single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: reagent role
      intersection of: Restriction
        on property: inheres in
        some values from: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: secondary structure of sequence macromolecule
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay
term editor: Person: Philippe Rocca-Serra
definition source: RNAO and OBI
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
editor preferred term: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
has curation status: IAO_0000122

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: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: rhodium atom
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: deoxyribonucleic acid
    union of: ribonucleic acid
example of usage: PMID:2843807
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: Rhodium DNA structure mapping assay
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhodium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Rhodium probe
has curation status: IAO_0000122

RNA ADA I RNA structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000003745
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:7527340
term editor: Person: Philippe Rocca-Serra
editor preferred term: RNA ADA I RNA structure mapping assay
definition source: RNA ontology
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNA adenosine deaminase I as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNA adenosine deaminase I
has curation status: IAO_0000122

Lead structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: lead(0)
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: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: 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
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Lead probe
has curation status: IAO_0000122

RNASE T2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000014060
example of usage: PMID:6207483
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE T2 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse T2
has curation status: IAO_0000122

gene dosage assay
type: Class
subclass of: assay
definition source: David Osumi Sutherland
term editor: PERSON: Bjoern Peters
definition: an assay of changes in phenotype due to increased or decreased dosage of a single allele of a gene.
editor preferred term: gene dosage assay
has curation status: IAO_0000120

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_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: (S)-1-(4-bromoacetamidobenzyl)EDTA
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
editor preferred term: Fe-BABE RNA structure mapping assay
example of usage: PMID: 7862644
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Fe-BABE probe
has curation status: IAO_0000122

RNASE U2 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025475
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:409999
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE U2 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse U2
has curation status: IAO_0000122

binding constant determination assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: binding constant
subclass of: binding assay
example of usage: Determination of KD value for an antibody binding a protein using a BIACORE assay.
definition: A binding assay where the specified output is a binding constant
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
editor preferred term: binding constant determination assay
has curation status: IAO_0000123

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: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: N-methylisatoic anhydride
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
editor preferred term: NMIA RNA structure mapping assay
example of usage: PMID: 15796531
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
alternative term: SHAPE mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using NMIA probe
has curation status: IAO_0000122

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: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: terbium atom
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
example of usage: PMID:10772868
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: Terbium RNA structure mapping assay
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using Terbium probe
has curation status: IAO_0000122

feature extraction
type: Class
subclass of: OBI_0200000
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  some values from: image
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200005
definition: A planed process with objective of obtaining quantified values from an image.
definition source: MO_928: feature_extraction
term editor: PERSON: Jie Zheng
editor preferred term: feature extraction
has curation status: IAO_0000123

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: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: hydroxyl
alternative term: MOHCA assay
alternative term: OH footprinting assay
editor preferred term: OH-radical structure mapping assay
example of usage: PMID:2501870
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
definition: a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using OH-radical probe
has curation status: IAO_0000122

RNASE T1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025467
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
example of usage: PMID:114514
term editor: Person:Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: RNASE T1 structure mapping assay
definition: a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
alternative term: single nucleotide resolution mapping assay using RNAse T1
has curation status: IAO_0000122

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
definition: An image creation process that generate an image from the array.
definition source: MO_929: image_acquisition
term editor: PERSON: Jie Zheng
alternative term: array image acquisition
editor preferred term: array image creation
has curation status: IAO_0000123

light emission device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: light emission function
subclass of: 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)
definition source: OBI
term editor: Person:Helen Parkinson
definition: a device which has a function to emit light.
editor preferred term: light emission device
has curation status: IAO_0000120

perturbation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: perturb function
subclass of: device
example of usage: A homogenizer is a perturbation device.
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
editor preferred term: perturbation device
has curation status: IAO_0000123

environmental control device
type: Class
equivalent class: 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
example of usage: A growth chamber is an environmental control device.
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
editor preferred term: environmental control device
has curation status: IAO_0000120

Nuclease S1 structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of sequence macromolecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: catalytic activity
    intersection of: Restriction
      on property: inheres in
      some values from: PR_000025471
editor preferred term: Nuclease S1 structure mapping assay
example of usage: PMID:363143
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
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
alternative term: single nucleotide resolution mapping assay using Nuclease S1
has curation status: IAO_0000122

specimen fixation function
type: Class
subclass of: function
term editor: EAGLE-I
definition: a function that allows specific identification of individual speciment from one another.
example of usage: e.g the function of a bar code reader used to read slide bar codes
editor preferred term: specimen fixation function
has curation status: IAO_0000123

obsolete_specimen fixation function
type: Class
subclass of: ObsoleteClass
definition: A specimen fixation function is a function that holds or fastens an entity in a fixed position.
term editor: EAGLE-I
comment: duplicate term
editor preferred term: obsolete_specimen fixation function
deprecated: true
has curation status: IAO_0000123
has obsolescence reason: IAO_0000227

Ruthenium structure mapping assay
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
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: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: ruthenium atom
example of usage: PMID:3016894
term editor: Person:Philippe Rocca-Serra
definition source: RNAOntology
editor preferred term: Ruthenium structure mapping assay
definition: is a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhutenium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
has curation status: IAO_0000122

inline probing RNA structure mapping
type: Class
subclass of: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: reagent role
    intersection of: Restriction
      on property: inheres in
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: secondary structure of RNA molecule
subclass of: Restriction
  on property: has_specified_input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
example of usage: PMID:10573122 and PMID: 18369975
term editor: Person: Philippe Rocca-Serra
definition source: RNA ontology
editor preferred term: inline probing RNA structure mapping
definition: is a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses intromolecular reactivity to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
has curation status: IAO_0000122

current amplification function
type: Class
subclass of: function
definition: A current amplification function is an amplification function that increases the amplitude of a current.
term editor: EAGLE-I
editor preferred term: current amplification function
has curation status: IAO_0000123

stabilization function
type: Class
subclass of: function
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 term: isolation function
editor preferred term: stabilization function
has curation status: IAO_0000123

pump function
type: Class
subclass of: transfer function
term editor: EAGLE-I
definition: a transfer unction where the transfer requires work to move the entity, often against a gradient.
editor preferred term: pump function
has curation status: IAO_0000123

cell transfer function
type: Class
subclass of: transfer function
example of usage: A cell harvester has a cell transfer function.
term editor: EAGLE-I
editor preferred term: cell transfer function
definition: is a transfer function that displaces cells from one place to another
has curation status: IAO_0000123

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
definition: A device that records the patterns of pulse waves inside blood vessels.
term editor: PERSON: Erik Segerdell
editor preferred term: angiograph
definition source: http://medical-dictionary.thefreedictionary.com/angiograph
has curation status: IAO_0000120

capillary blotter
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
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
editor preferred term: capillary blotter
definition source: http://www.biometra.de/
has curation status: IAO_0000120

bioreactor
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: environment control function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT
term editor: PERSON: Erik Segerdell
editor preferred term: bioreactor
definition source: http://en.wikipedia.org/wiki/Bioreactor
has curation status: IAO_0000120

pH meter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: pH meter
has curation status: IAO_0000120

digital camera
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
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
editor preferred term: digital camera
definition source: http://en.wikipedia.org/wiki/Digital_camera
has curation status: IAO_0000120

chip spotting device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
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
editor preferred term: chip spotting device
has curation status: IAO_0000120

RNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
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
editor preferred term: RNA extraction/purification instrument
has curation status: IAO_0000120

DNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA extraction
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
editor preferred term: DNA extract
definition source: Group: UPenn group
term editor: Person: Jie Zheng
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
has curation status: IAO_0000120

two-photon laser/detector
type: Class
subclass of: OBI_0400065
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
editor preferred term: two-photon laser/detector
has curation status: IAO_0000120

electrophoresis system
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
definition: A device that moves charged particles through a medium by using an electric field induced by electrodes.
term editor: PERSON: Erik Segerdell
editor preferred term: electrophoresis system
definition source: http://en.wikipedia.org/wiki/Category:Electrophoresis
has curation status: IAO_0000120

PET synthesizer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: synthesizing function
definition: A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: PET synthesizer
has curation status: IAO_0000120

spinning-disk confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: spinning-disk confocal microscope
has curation status: IAO_0000120

DNA synthesizer
type: Class
subclass of: OBI_0400113
definition: An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
editor preferred term: DNA synthesizer
term editor: PERSON: Erik Segerdell
definition source: http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers
has curation status: IAO_0000120

high performance liquid chromatography instrument
type: Class
subclass of: liquid chromatography instrument
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
editor preferred term: high performance liquid chromatography instrument
definition source: http://en.wikipedia.org/wiki/High_performance_liquid_chromatography
has curation status: IAO_0000120

microplate reader
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: microplate reader
has curation status: IAO_0000120

ELISA microplate reader
type: Class
subclass of: microplate reader
definition: A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
editor preferred term: ELISA microplate reader
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
has curation status: IAO_0000120

spot cutter
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A robotic device that is used to excise spots from gels.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: spot cutter
has curation status: IAO_0000120

microwave synthesis system
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: synthesizing function
subclass of: Restriction
  on property: has function
  some values from: excitation function
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
editor preferred term: microwave synthesis system
has curation status: IAO_0000120

densitometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: densitometer
definition source: http://en.wikipedia.org/wiki/Densitometer
has curation status: IAO_0000120

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
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
editor preferred term: automatic staining machine
has curation status: IAO_0000120

automatic tissue processor
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: reagent application function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: automatic tissue processor
has curation status: IAO_0000120

stereo microscope
type: Class
subclass of: optical microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: stereo microscope
has curation status: IAO_0000120

top loading balance
type: Class
subclass of: balance
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
editor preferred term: top loading balance
has curation status: IAO_0000120

perfusion station
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: specimen fixation function
definition: A device or system in which perfusion units are integrated.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: perfusion station
has curation status: IAO_0000120

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
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
editor preferred term: SPECT scanner
definition source: http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography
has curation status: IAO_0000120

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
definition: a manufacturer role which is played by the person or organization that manufactured the array
definition source: MO_695 array_manufacturer
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: array manufacturer role
has curation status: IAO_0000120

scintillation counter
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A device that is used to measure ionizing radiation.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Scintillation_counter
editor preferred term: scintillation counter
has curation status: IAO_0000120

programmable array microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: programmable array microscope
has curation status: IAO_0000120

cryostat
type: Class
subclass of: container
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: cool function
subclass of: Restriction
  on property: has function
  some values from: contain function
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
editor preferred term: cryostat
definition source: http://en.wikipedia.org/wiki/Cryostat
has curation status: IAO_0000120

microtome knife maker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: microtome knife maker
has curation status: IAO_0000120

cryofixation device
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: specimen fixation function
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
editor preferred term: cryofixation device
definition source: http://en.wikipedia.org/wiki/Cryofixation
has curation status: IAO_0000120

hybridization oven
type: Class
subclass of: incubator
subclass of: Restriction
  on property: has function
  some values from: mechanical function
subclass of: Restriction
  on property: has function
  some values from: contain function
definition: A device that creates an appropriate environment for nucleic acid hybridization.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: hybridization oven
has curation status: IAO_0000120

incubator shaker
type: Class
subclass of: OBI_0002089
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
definition: An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: incubator shaker
has curation status: IAO_0000120

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
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
editor preferred term: small-animal image acquisition device
has curation status: IAO_0000120

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
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
editor preferred term: infrared image acquisition device
has curation status: IAO_0000120

confocal microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: confocal microscope
definition source: http://en.wikipedia.org/wiki/Confocal_microscopy
has curation status: IAO_0000120

patch clamp device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: patch clamp device
has curation status: IAO_0000120

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
definition: A device that is used to acquire images of laboratory gels.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: gel imaging system
has curation status: IAO_0000120

protein separation apparatus
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
definition: A device that is used for the separation of proteins.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: protein separation apparatus
has curation status: IAO_0000120

multichannel electronic pipette
type: Class
subclass of: multichannel pipette
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
editor preferred term: multichannel electronic pipette
has curation status: IAO_0000120

vitrification apparatus
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: vitrification apparatus
has curation status: IAO_0000120

radiography instrument
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
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
editor preferred term: radiography instrument
has curation status: IAO_0000120

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
definition: A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: radiation measurement device
has curation status: IAO_0000120

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
definition: A device that is used to freeze dry material.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Freeze_drying
editor preferred term: lyophilizer
has curation status: IAO_0000120

tandem mass spectrometer
type: Class
subclass of: mass spectrometer
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
editor preferred term: tandem mass spectrometer
has curation status: IAO_0000120

microhardness tester
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A hardness testing device that is used in light-optical microscopes.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 4611487
editor preferred term: microhardness tester
has curation status: IAO_0000120

multimode microplate reader
type: Class
subclass of: microplate reader
definition: A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: multimode microplate reader
has curation status: IAO_0000120

mechanical balance
type: Class
subclass of: balance
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
editor preferred term: mechanical balance
has curation status: IAO_0000120

computer cluster
type: Class
subclass of: OBI_0400107
definition: A group of linked computers, working together closely so that in many respects they form a single computer.
term editor: PERSON: Erik Segerdell
editor preferred term: computer cluster
definition source: http://en.wikipedia.org/wiki/Cluster_(computing)
has curation status: IAO_0000120

microtome knife sharpener
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A device that is used to sharpen knives used in microtomy.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: microtome knife sharpener
has curation status: IAO_0000120

plate shaker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A device that provides shaking motion for microplates.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: plate shaker
has curation status: IAO_0000120

coagulation analyzer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: A device for automatically analyzing blood coagulation in a clinical laboratory.
term editor: PERSON: Erik Segerdell
definition source: United States Patent 5439646
editor preferred term: coagulation analyzer
has curation status: IAO_0000120

laser capture microdissection microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: laser capture microdissection microscope
has curation status: IAO_0000120

liquid extraction robot
type: Class
subclass of: OBI_0400112
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A liquid handling device that provides automatic liquid extraction.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: liquid extraction robot
has curation status: IAO_0000120

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
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
editor preferred term: ultrasound machine
has curation status: IAO_0000120

immunoblot scanner
type: Class
subclass of: image creation device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: image acquisition function
definition: A device that is used for the imaging of immunoblots.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: immunoblot scanner
has curation status: IAO_0000120

microcentrifuge
type: Class
subclass of: OBI_0400106
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
editor preferred term: microcentrifuge
has curation status: IAO_0000120

electronic repeater pipette
type: Class
subclass of: micropipette
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
editor preferred term: electronic repeater pipette
definition source: http://www.faqs.org/patents/app/20090196797
has curation status: IAO_0000120

electron paramagnetic resonance spectrometer
type: Class
subclass of: OBI_0400115
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
editor preferred term: electron paramagnetic resonance spectrometer
definition source: http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
has curation status: IAO_0000120

rocker
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: rocker
has curation status: IAO_0000120

analytical balance
type: Class
subclass of: balance
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
editor preferred term: analytical balance
definition source: http://en.wikipedia.org/wiki/Weighing_scale
has curation status: IAO_0000120

scanning force microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: scanning force microscope
has curation status: IAO_0000120

pulsed-field gel electrophoresis system
type: Class
subclass of: gel electrophoresis system
definition: A gel electrophoresis system that is used to separate very large molecules of DNA.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
editor preferred term: pulsed-field gel electrophoresis system
has curation status: IAO_0000120

tissue embedding station
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A device that is used to perform paraffin embedding of tissue specimens.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: tissue embedding station
has curation status: IAO_0000120

nucleic acid sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: nucleic acid sequencer
has curation status: IAO_0000120

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
definition: A device that is used to acquire and image bead array data.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: bead array reader
has curation status: IAO_0000120

real-time PCR machine
type: Class
subclass of: PCR instrument
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
editor preferred term: real-time PCR machine
has curation status: IAO_0000120

paraffin oven
type: Class
subclass of: container
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: contain function
definition: A device that is used for the warming of paraffin embedding medium.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: paraffin oven
has curation status: IAO_0000120

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
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.
definition source: J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
term editor: PERSON: Erik Segerdell
editor preferred term: autoclave
has curation status: IAO_0000120

microplate washer
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: microplate washer
has curation status: IAO_0000120

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
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
editor preferred term: nucleic acid extraction/purification instrument
has curation status: IAO_0000120

ELISA microplate washer
type: Class
subclass of: microplate washer
definition: A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
editor preferred term: ELISA microplate washer
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
has curation status: IAO_0000120

vacuum manifold
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: vacuum manifold
has curation status: IAO_0000120

DNA extraction/purification instrument
type: Class
subclass of: nucleic acid extraction/purification instrument
definition: A device that is used to isolate and collect DNA for subsequent molecular analysis.
editor preferred term: DNA extraction/purification instrument
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/DNA_extraction
has curation status: IAO_0000120

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
definition: A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: multichannel pipette
has curation status: IAO_0000120

cell harvester
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: cell transfer function
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
editor preferred term: cell harvester
has curation status: IAO_0000120

portable fluorometer
type: Class
subclass of: OBI_0400143
definition: A compact fluorometer that can be carried or moved with ease.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: portable fluorometer
has curation status: IAO_0000120

gel electrophoresis system
type: Class
subclass of: electrophoresis system
definition: A device that moves charged particles through a medium by using an electric field induced by electrodes.
term editor: PERSON: Erik Segerdell
alternative term: electrophoresis system
editor preferred term: gel electrophoresis system
definition source: http://en.wikipedia.org/wiki/Category:Electrophoresis
has curation status: IAO_0000120

diffractometer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: diffractometer
definition source: http://en.wikipedia.org/wiki/Diffractometer
has curation status: IAO_0000120

microdissection instrument
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: microdissection instrument
has curation status: IAO_0000120

micropipette puller
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A device that is used to fabricate glass micropipettes.
term editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Micropipette
editor preferred term: micropipette puller
has curation status: IAO_0000120

laser scanning confocal microscope
type: Class
subclass of: confocal microscope
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: laser scanning confocal microscope
has curation status: IAO_0000120

digital microscope
type: Class
subclass of: OBI_0400169
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: digital microscope
definition source: http://en.wikipedia.org/wiki/Digital_microscope
has curation status: IAO_0000120

freeze substitution system
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: freeze function
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
editor preferred term: freeze substitution system
has curation status: IAO_0000120

micropipette
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
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
editor preferred term: micropipette
has curation status: IAO_0000120

voltage clamp device
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: voltage clamp device
has curation status: IAO_0000120

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
definition: A device that heats materials in a vacuum.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: vacuum oven
has curation status: IAO_0000120

slide warmer
type: Class
subclass of: environmental control device
subclass of: Restriction
  on property: has function
  some values from: heat function
definition: A device that is used to heat microscope slides.
term editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
editor preferred term: slide warmer
has curation status: IAO_0000120

capillary electrophoresis instrument
type: Class
subclass of: electrophoresis system
definition: An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
term editor: PERSON: Erik Segerdell
editor preferred term: capillary electrophoresis instrument
definition source: http://en.wikipedia.org/wiki/Capillary_electrophoresis
has curation status: IAO_0000120

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
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
editor preferred term: denaturing high-performance liquid chromatography instrument
definition source: doi:10.1385/1-59259-850-1:173
has curation status: IAO_0000120

agarose gel electrophoresis system
type: Class
subclass of: electrophoresis system
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
editor preferred term: agarose gel electrophoresis system
definition source: http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
has curation status: IAO_0000120

balance
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
definition: A measuring instrument that is used to determine the weight or mass of an object.
term editor: PERSON: Erik Segerdell
editor preferred term: balance
definition source: http://en.wikipedia.org/wiki/Weighing_scale
has curation status: IAO_0000120

surface plasmon resonance instrument
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
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
editor preferred term: surface plasmon resonance instrument
has curation status: IAO_0000120

protein sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
definition: An device that is used to determine the order of amino acids in protein sequences.
definition source: PERSON: Erik Segerdell
term editor: PERSON: Erik Segerdell
editor preferred term: protein sequencer
has curation status: IAO_0000120

X-ray source
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: excitation function
definition: A device that is used to generate X-rays.
term editor: PERSON: Erik Segerdell
editor preferred term: X-ray source
definition source: http://en.wikipedia.org/wiki/X-ray_generator
alternative term: x-ray generator
has curation status: IAO_0000120

liquid chromatography instrument
type: Class
subclass of: chromatography device
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
editor preferred term: liquid chromatography instrument
has curation status: IAO_0000120

spike-in quality control role
type: Class
subclass of: reference substance role
definition source: MO_937 spike_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
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
editor preferred term: spike-in quality control role
has curation status: IAO_0000120

individual organism identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: OBI_0100026
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_169 Individual
definition: a CRID symbol used to distinguish one individual organism from another.
editor preferred term: individual organism identifier
has curation status: IAO_0000120

dye swap quality control role
type: Class
subclass of: reference substance role
subclass of: Restriction
  on property: inheres in
  some values from: labeled nucleic acid extract
definition source: MO_524 dye_swap_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng
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
editor preferred term: dye swap quality control role
has curation status: IAO_0000120

labeled nucleic acid extract
type: Class
subclass of: labeled specimen
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
subclass of: Class
  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 role
    some values from: specimen role
definition source: MO_221 labeledExtract
term editor: Person: Jie Zheng
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.
alternative term: labeled extract
ISA alternative term: labeled extract
editor preferred term: labeled nucleic acid extract
has curation status: IAO_0000120

binding constant
type: Class
equivalent class: Class
  union of: equilibrium dissociation constant (KD)
  union of: equilibrium association constant (KA)
  union of: equilibrium dissociation constant (KD) approximated by IC50
  union of: equilibrium dissociation constant (KD) approximated by EC50
  union of: half life of binding datum
  union of: binding off rate measurement datum (koff)
  union of: binding on rate measurement datum (kon)
subclass of: binding datum
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.
definition: A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
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".
editor preferred term: binding constant
has curation status: IAO_0000123

3D structure determination of bound complex assay
type: Class
equivalent class: Class
  intersection of: OBI_0600045
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: binding
subclass of: binding assay
subclass of: OBI_0600045
editor preferred term: 3D structure determination of bound complex assay
definition: A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration.
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.
definition source: IEDB
term editor: IEDB
has curation status: IAO_0000120

binding 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: binding
subclass of: assay
definition: An assay with the objective to characterize the disposition of two or more material entities to form a complex.
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.nnThe 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.
definition source: PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
term editor: PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
editor preferred term: binding assay
has curation status: IAO_0000120

cell culture expansion
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
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
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.
definition source: MO_758 grow
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a processual entity that results in the increase of cell numbers
editor preferred term: cell culture expansion
editor note: including grow of yeast and bacteria
has curation status: IAO_0000120

gene knock out
type: Class
subclass of: OBI_0600043
definition source: MO_771 gene_knock_out
term editor: PERSON: Chris Stoeckert, Jie Zheng
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.
editor preferred term: gene knock out
has curation status: IAO_0000120

gene knock in
type: Class
subclass of: OBI_0600043
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
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.
editor preferred term: gene knock in
has curation status: IAO_0000120

chromosomal substitution
type: Class
subclass of: OBI_0600043
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'.
definition source: MO_995 chromosomal_substitution
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: chromosomal substitution
has curation status: IAO_0000120

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
definition source: GROUP: OBI
term editor: PERSON: Jie Zheng
definition: a material entity, organism or cell, that is the output of a genetic transformation process.
editor preferred term: genetically modified material
curator note: term is proposed by BP on Oct 25, 2010 dev call
has curation status: IAO_0000120

transfection
type: Class
subclass of: OBI_0600043
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: bearer of
      some values from: target of material addition role
subclass of: Restriction
  on property: has part
  some values from: OBI_0600033
definition source: MO_366 transfection
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
editor preferred term: transfection
has curation status: IAO_0000120

genetic transformation objective
type: Class
subclass of: material transformation objective
curator note: suggested to be added by BP and AR during Oct 25, 2010 dev call
term editor: Person: Jie Zheng
definition source: Person: Jie Zheng
definition: a material transformation objective aims to create genetically modified organism or cell
editor preferred term: genetic transformation objective
has curation status: IAO_0000120

induced mutation
type: Class
subclass of: OBI_0600043
definition source: MO_564 induced_mutation
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
editor preferred term: induced mutation
has curation status: IAO_0000120

3D structural organization datum
type: Class
subclass of: measurement datum
editor preferred term: 3D structural organization datum
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
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

age since planting measurement datum
type: Class
subclass of: age measurement datum
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.
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
definition source: MO_495 planting
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since planting measurement datum
has curation status: IAO_0000120

age since hatching measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_745 hatching
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since hatching measurement datum
has curation status: IAO_0000120

age measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: age measurement datum
definition: An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
definition source: OBI group
term editor: PERSON: Alan Ruttenberg
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.
editor preferred term: age measurement assay
has curation status: IAO_0000120

age since egg laying measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_767 egg laying
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since egg laying measurement datum
has curation status: IAO_0000120

assay validation objective
type: Class
subclass of: objective specification
definition source: GROUP: Penn Group
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
editor preferred term: assay validation objective
has curation status: IAO_0000120

age since germination measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_590 germination
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since germination measurement datum
has curation status: IAO_0000120

validation by reverse transcription PCR design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: assay validation objective
    intersection of: Restriction
      on property: objective_achieved_by
      some values from: reverse transcription polymerase chain reaction assay
definition source: MO_986 reverse_transcription_PCR_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng
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
editor preferred term: validation by reverse transcription PCR design
has curation status: IAO_0000120

age since eclosion measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_876 eclosion
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since eclosion measurement datum
has curation status: IAO_0000120

age since sowing measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_748 sowing
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since sowing measurement datum
has curation status: IAO_0000120

age since coitus measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_783 coitus
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since coitus measurement datum
has curation status: IAO_0000120

validation by real time PCR design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: assay validation objective
    intersection of: Restriction
      on property: objective_achieved_by
      some values from: real time polymerase chain reaction assay
definition source: MO_434 real_time_PCR_quality_control
term editor: PERSON: Chris Stoeckert, Jie Zheng
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
editor preferred term: validation by real time PCR design
has curation status: IAO_0000120

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: PATO_0000011
subclass of: Restriction
  on property: is_specified_output_of
  some values from: age measurement assay
definition: A time measurement datum that is the result of measurement of age of an organism
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
definition source: MO_178 Age
term editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.
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
editor preferred term: age measurement datum
has curation status: IAO_0000120

age since fertilization measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_701 fertilization
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since fertilization measurement datum
has curation status: IAO_0000120

age since birth measurement datum
type: Class
subclass of: age measurement datum
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.
definition source: MO_710 birth
term editor: PERSON:Chris Stoeckert, Jie Zheng
editor preferred term: age since birth measurement datum
has curation status: IAO_0000120

reverse transcription polymerase chain reaction assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: ribonucleic acid
    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: information content entity
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: has part
  some values from: reverse transcribed polymerase chain reaction
definition source: GROUP: Penn Group
term editor: PERSON: Chris Stoeckert, Jie Zheng
definition: an assay that evaluates 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.
editor preferred term: reverse transcription polymerase chain reaction assay
has curation status: IAO_0000120

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
term editor: Bjoern Peters
definition source: Bjoern Peters
definition: The time it takes for 50% of a class of stochastic processes to occur.
editor preferred term: half life datum (t 1/2)
alternative term: t 1/2
has curation status: IAO_0000120

dose response curve
type: Class
subclass of: line graph
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
editor preferred term: dose response curve
has curation status: IAO_0000120

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
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
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
editor preferred term: service
has curation status: IAO_0000120

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: inheres in
      some values from: OBI_1110022
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.
term editor: PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
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.
alternative term: adoptive transfer
editor preferred term: passive immunization
has curation status: IAO_0000122

selective organism creation objective
type: Class
subclass of: objective specification
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
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.
editor preferred term: selective organism creation objective
has curation status: IAO_0000120

Individual epitope immunization in vivo
type: Class
subclass of: OBI_1110015
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.
definition: An immunization in which an individual epitope is administered into a host organism.
editor preferred term: Individual epitope immunization in vivo
example of usage: Injection of a peptide T cell epitope into a mouse
term editor: PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita
has curation status: IAO_0000120

RNA sequencing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: ribonucleic acid
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
  intersection 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: primary structure of RNA molecule
subclass of: OBI_0600047
editor note: BP 12/21:Created based on a request from Melanie
definition source: Bjoern Peters
term editor: Bjoern Peters
editor preferred term: RNA sequencing
definition: RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
has curation status: IAO_0000120

efficacy of epitope intervention experiment
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: OBI_1110001
subclass of: Restriction
  on property: has part
  some values from: epitope specific immune intervention
definition: An experiment that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism.
term editor: Bjoern Peters
editor preferred term: efficacy of epitope intervention experiment
IEDB alternative term: efficacy of in vivo intervention
has curation status: IAO_0000120

epitope protection from infectious challenge experiment
type: Class
subclass of: epitope protection experiment
subclass of: Restriction
  on property: has part
  some values from: pathogen challenge
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
editor preferred term: epitope protection from infectious challenge experiment
IEDB alternative term: protection from infectious challenge
has curation status: IAO_0000120

half maximal effective concentration (EC50)
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is about
  some values from: dose response curve
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
term editor: Bjoern Peters; Randi Vita
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.
editor preferred term: half maximal effective concentration (EC50)
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.
definition source: wikipedia
has curation status: IAO_0000120

binding datum
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is about
    some values from: binding
subclass of: data item
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
editor preferred term: binding datum
has curation status: IAO_0000120

negative binding datum
type: Class
subclass of: binding datum
definition: A binding datum that states that there is no significant disposition of two or more entities to form a complex
editor preferred term: negative binding datum
has curation status: IAO_0000123

epitope protection from tumor challenge experiment
type: Class
subclass of: epitope protection experiment
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
editor preferred term: epitope protection from tumor challenge experiment
IEDB alternative term: tumor burden after challenge
has curation status: IAO_0000120

epitope protection experiment
type: Class
subclass of: efficacy of epitope intervention experiment
term editor: Bjoern Peters
definition: an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
editor preferred term: epitope protection experiment
IEDB alternative term: protection from challenge
has curation status: IAO_0000120

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
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
definition source: MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
alternative term: cultivar
alternative term: ecotype
alternative term: strain
editor preferred term: selectively maintained organism
has curation status: IAO_0000120

epitope protection from infectious challenge experiment based on pathogen burden
type: Class
subclass of: epitope protection from infectious challenge experiment
subclass of: Restriction
  on property: has part
  some values from: infectious agent detection assay
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
editor preferred term: epitope protection from infectious challenge experiment based on pathogen burden
IEDB alternative term: pathogen burden after infectious challenge
has curation status: IAO_0000120

infectious agent detection assay
type: Class
subclass of: assay
editor note: 2/22/2011, BP: This should probably be an analyte assay, but the logical definition of those is currently restricted to 'scattered molecular aggregates', which excludes using infectious agents as analytes. See below (realizes some ('evaluant role' and (role_of some material_entity))) and (realizes some ('analyte role' and (role_of some 'infectious agent'))) and (achieves_planned_objective some 'analyte measurement objective')
definition: An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant
term editor: Bjoern Peters, Randi Vita, Jason Greenbaum
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.
editor preferred term: infectious agent detection assay
has curation status: IAO_0000120

epitope disease exacerbation experiment
type: Class
subclass of: efficacy of epitope intervention experiment
term editor: Bjoern Peters
definition: an epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
editor preferred term: epitope disease exacerbation experiment
IEDB alternative term: exacerbation assay
has curation status: IAO_0000120

epitope protection experiment based on survival
type: Class
subclass of: epitope protection experiment
subclass of: Restriction
  on property: has part
  some values from: survival assessment
term editor: Bjoern Peters
definition: an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
editor preferred term: epitope protection experiment based on survival
IEDB alternative term: host survival after challenge
has curation status: IAO_0000120

epitope treatment experiment
type: Class
subclass of: efficacy of epitope intervention experiment
term editor: Bjoern Peters
definition: an epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
IEDB alternative term: decreased disease symptoms after treatment
editor preferred term: epitope treatment experiment
has curation status: IAO_0000120

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
term editor: Bjoern Peters; Randi Vita
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.
example of usage: Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
editor preferred term: half maximal inhibitory concentration (IC50)
definition source: wikipedia
has curation status: IAO_0000120

epitope specific immune intervention
type: Class
subclass of: passive immunization
subclass of: Class
  union of: passive immunization
  union of: Individual epitope immunization in vivo
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
editor preferred term: epitope specific immune intervention
has curation status: IAO_0000120

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
definition: A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific cytokine production by T cells
has curation status: IAO_0000122

ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
definition: An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TGFb release|ELISPOT
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that assesses the operator performance and relation to data consistency and quality.
definition source: MO_519 operator_variation_design
editor preferred term: operator variation design
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific IP-10 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific IP-10 production by T cells
definition: An assay of epitope specific IP-10 production by T cells that uses a cytometric bead array assay.
IEDB alternative term: CXCL10/IP-10 release|cytometric bead array
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific IP-10 production by T cells
has curation status: IAO_0000120

comparative genome hybridization by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: comparative genomic hybridization by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that detects genomic copy number variations using microarray technology.
definition source: MO_856 comparative_genome_hybridization_design
editor preferred term: comparative genome hybridization by array design
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-27 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-27 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells.
definition source: IEDB
IEDB alternative term: IL-27 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-27 production by T cells
has curation status: IAO_0000120

in vivo design
type: Class
subclass of: OBI_0500000
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
definition source: MO_454 in_vivo_design
editor preferred term: in vivo design
has curation status: IAO_0000120

genotyping by high throughput sequencing design
type: Class
subclass of: genotyping design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: genotyping by high throughput sequencing assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400103
definition source: MO_560 genotyping_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
editor preferred term: genotyping by high throughput sequencing design
has curation status: IAO_0000120

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
definition: A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific tolerance induction by T cells
has curation status: IAO_0000122

innate behavior design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
definition source: MO_355 innate_behavior_design
editor preferred term: innate behavior design
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
definition: An assay of epitope specific transforming growth factor-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TGFb release|RNA/DNA detection
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

SNP microarray
type: Class
subclass of: OBI_0400148
definition source: EFO_0002703 SNP array
term editor: Person: Helen Parkinson
definition: a DNA microarray used to detect polymorphisms in DNA samples
editor preferred term: SNP microarray
has curation status: IAO_0000120

cell component comparison 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: cellular_component
subclass of: Restriction
  on property: has part
  some values from: cellular feature identification objective
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
editor preferred term: cell component comparison design
has curation status: IAO_0000120

ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
IEDB alternative term: GM-CSF release|ELISPOT
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

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
definition: A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000122

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
definition: A process of T cell activation resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific T cell activation
has curation status: IAO_0000122

biological activity assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-10 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells.
definition source: IEDB
IEDB alternative term: IL-10 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
definition: An assay of epitope specific transforming growth factor-beta production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TGFb release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120

ex vivo design
type: Class
subclass of: OBI_0500000
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_808 ex_vivo_design
editor preferred term: ex vivo design
has curation status: IAO_0000120

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
definition: A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific type IV hypersensitivity by T cells
has curation status: IAO_0000122

normalization testing 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: OBI_0200169
subclass of: Restriction
  on property: has part
  some values from: software testing objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that tests different normalization procedures.
definition source: MO_729 normalization_testing_design
editor preferred term: normalization testing design
has curation status: IAO_0000120

intracellular material detection assay measuring epitope specific perforin release
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific perforin release by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific perforin release by T cells
definition: A T cell epitope specific perforin release assay that uses an intracellular material detection by flow cytometry assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular material detection assay measuring epitope specific perforin release
IEDB alternative term: perforin release|intracellular staining
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-2 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-2 production by T cells
definition: An assay of epitope specific interleukin-2 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-2 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-22 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells.
definition source: IEDB
IEDB alternative term: IL-22 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-22 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-8 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells.
definition source: IEDB
IEDB alternative term: IL-8 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-8 production by T cells
has curation status: IAO_0000120

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
definition: A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000122

cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-10 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-10 production by T cells
definition: An assay of epitope specific interleukin-10 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-10 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120

ChIP-chip by SNP array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Restriction
  on property: has participant
  some values from: SNP microarray
term editor: Group: ArrayExpress production team
definition: An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology
editor preferred term: ChIP-chip by SNP array assay
definition source: EFO_0002764 ChIP-chip by SNP array
has curation status: IAO_0000120

ELISA measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific RANTES production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific RANTES production by T cells
definition: An assay of epitope specific RANTES production by T cells that uses an ELISA.
IEDB alternative term: CCL5/RANTES release|ELISA
editor preferred term: ELISA measuring epitope specific RANTES production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-1 beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-1 beta production by T cells
definition: An assay of epitope specific interleukin-1 beta production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-1b release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
has curation status: IAO_0000120

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: part of
  some values from: genotype information
definition source: Group: OBI group
term editor: Group: OBI group
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
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
editor note: proposed and discussed on San Diego OBI workshop, March 2011
has curation status: IAO_0000120

environmental history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
definition source: MO_698 environmental_history_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
editor preferred term: environmental history design
has curation status: IAO_0000120

ELISPOT assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-6 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific interleukin-6 production by T cells
definition: An assay of epitope specific interleukin-6 production by T cells that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific interleukin-6 production by T cells
definition source: IEDB
IEDB alternative term: IL-6 release|ELISPOT
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
type: Class
subclass of: biological activity assay measuring epitope specific T cell helper activity
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|biological activity
editor preferred term: biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
has curation status: IAO_0000120

plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: OBI_0002097
  intersection of: Restriction
    on property: has part
    some values from: surface plasmon resonance binding assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: OBI_0002097
definition: A T cell epitope equilibrium dissociation constant (KD) determination assay that uses a surface plasmon resonance assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: dissociation constant KD|surface plasmon resonance (SPR)|nM
editor preferred term: plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-5 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells.
definition source: IEDB
IEDB alternative term: IL-5 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
definition: An assay of epitope specific transforming growth factor-beta production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific transforming growth factor-beta production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TGFb release|ELISA
has curation status: IAO_0000120

biological activity assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: chemokine (C-C motif) ligand 5 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects RANTES production by T cells.
IEDB alternative term: CCL5/RANTES release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific RANTES production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: granulocyte macrophage colony-stimulating factor production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells.
IEDB alternative term: GM-CSF release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
has curation status: IAO_0000120

epigenetic modification identification objective
type: Class
subclass of: molecular feature identification objective
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
editor preferred term: epigenetic modification identification objective
has curation status: IAO_0000120

transcription profiling by tiling array assay
type: Class
subclass of: transcription profiling assay
subclass of: Restriction
  on property: has participant
  some values from: tiling microarray
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
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: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
term editor: Person: James Malone
definition: An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
definition source: EFO_0002769 transcription profiling by tiling array
editor preferred term: transcription profiling by tiling array assay
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-22 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-22 production by T cells
definition: An assay of epitope specific interleukin-22 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-22 production by T cells
definition source: IEDB
IEDB alternative term: IL-22 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-21 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells.
definition source: IEDB
IEDB alternative term: IL-21 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-21 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring interleukin-9 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring interleukin-9 production by T cells
definition: An assay of epitope specific interleukin-9 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-9 production by T cells
definition source: IEDB
IEDB alternative term: IL-9 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

transcription profiling by high throughput sequencing design
type: Class
subclass of: transcription profiling design
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: RNA-seq assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400103
term editor: Person: Chris Stoeckert, Jie Zheng
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
definition source: Group: ArrayExpress production team
editor preferred term: transcription profiling by high throughput sequencing design
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-6 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-6 production by T cells
definition: An assay of epitope specific interleukin-6 production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
IEDB alternative term: IL-6 release|ICS
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-4 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-4 production by T cells
definition: An assay of epitope specific interleukin-4 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-4 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
subclass of: OBI_0001788
definition: A T cell epitope specific tumor necrosis factor production assay that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNFa release|RNA/DNA detection
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
definition: An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a cytometric bead array assay.
IEDB alternative term: CCL2/MCP-1 release|cytometric bead array
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-23 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-23 production by T cells
definition: An assay of epitope specific interleukin-23 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-23 production by T cells
definition source: IEDB
IEDB alternative term: IL-23 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific perforin release by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific perforin release by T cells
definition: A T cell epitope specific perforin release assay that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
IEDB alternative term: perforin release|RNA/DNA detection
has curation status: IAO_0000120

ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNF release|ELISA
has curation status: IAO_0000120

genotyping by high throughput sequencing assay
type: Class
subclass of: genotyping assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
term editor: Person: James Malone
definition: An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
definition source: EFO_0002771: genotyping by high throughput sequencing
editor preferred term: genotyping by high throughput sequencing assay
has curation status: IAO_0000120

ChIP-chip assay
type: Class
subclass of: OBI_0001956
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: Class
        union of: chromatin remodeling
        union of: regulation of molecular function, epigenetic
        union of: sequence-specific DNA binding
        union of: transcription factor binding site
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
    intersection of: Restriction
      on property: has part
      some values from: protein complex
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: protein and DNA interaction identification objective
subclass of: Restriction
  on property: has part
  some values from: immunoprecipitation
alternative term: ChIP-on-chip assay
term editor: Person: James Malone
comment: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
definition: an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis.
editor preferred term: ChIP-chip assay
has curation status: IAO_0000120

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
definition: A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific T cell tolerance induction
has curation status: IAO_0000122

obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
type: Class
subclass of: ObsoleteClass
definition: An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: T cell degranulation by intracellular staining
editor preferred term: obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000227
term replaced by: flow cytometry assay

biological activity assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-13 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells.
definition source: IEDB
IEDB alternative term: IL-13 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120

array platform 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: microarray platform
subclass of: Restriction
  on property: has part
  some values from: methodology testing objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
definition source: MO_899 array_platform_variation_design
editor preferred term: array platform variation design
has curation status: IAO_0000120

biological activity assay measuring interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-9 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells.
definition source: IEDB
IEDB alternative term: IL-9 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring interleukin-9 production by T cells
has curation status: IAO_0000120

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
definition: A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-3 production by T cells
has curation status: IAO_0000122

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: biological activity assay measuring epitope specific interleukin-5 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-5 production by T cells
definition: An assay of epitope specific interleukin-5 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-5 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

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
definition: A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific lymphotoxin A production by T cells
has curation status: IAO_0000122

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
definition: A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-1 alpha production by T cells
has curation status: IAO_0000122

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: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: ChIP-seq assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400103
subclass of: Restriction
  on property: has part
  some values from: protein and DNA interaction identification objective
definition source: http://en.wikipedia.org/wiki/Chip-Sequencing
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.
editor preferred term: ChIP-seq design
term editor: Person: Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120

translational bias design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that characterizes the association of transcripts and translation machinery.
definition source: MO_939 translational_bias_design
editor preferred term: translational bias design
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-3 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-3 production by T cells
definition: An assay of epitope specific interleukin-3 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-3 production by T cells
definition source: IEDB
IEDB alternative term: IL-3 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-1 alpha production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-1 alpha production by T cells
definition: An assay of epitope specific interleukin-1 alpha production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-1 alpha production by T cells
definition source: IEDB
IEDB alternative term: IL-1a release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

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
definition: A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-27 production by T cells
has curation status: IAO_0000122

biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific T cell helper activity
  intersection 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: helper T cell enhancement of T cell mediated immune response
  intersection 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: Class
subclass of: biological activity assay measuring epitope specific T cell helper activity
definition: A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: T cell help|biological activity
editor preferred term: biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
has curation status: IAO_0000120

biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: transforming growth factor beta production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TGFb release|biological activity
editor preferred term: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120

FWER adjusted p-value
type: Class
subclass of: quantitative confidence value
editor preferred term: FWER adjusted p-value
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)
example of usage: http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
has curation status: IAO_0000122

DNA methylation profiling by high throughput sequencing assay
type: Class
equivalent class: Class
  intersection of: DNA methylation profiling assay
  intersection of: Restriction
    on property: has participant
    some values from: OBI_0400103
subclass of: DNA methylation profiling assay
definition source: EFO_0002761 methylation profiling by high throughput sequencing
term editor: Group: ArrayExpress production team, James Malone, Helen Parkinson
comment: Philippe Rocca-Serra
definition: An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
editor preferred term: DNA methylation profiling by high throughput sequencing assay
has curation status: IAO_0000120

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
definition: A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000122

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: biological activity assay measuring epitope specific interleukin-12 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-12 production by T cells
definition: An assay of epitope specific interleukin-12 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-12 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

biological activity assay measuring epitope specific cytotoxic T cell degranulation
type: Class
equivalent class: Class
  intersection of: OBI_0002055
  intersection 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: cytotoxic T cell degranulation
subclass of: OBI_0002055
definition: A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific cytotoxic T cell degranulation
IEDB alternative term: degranulation|biological activity
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
definition: An assay of epitope specific transforming growth factor-beta production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TGFb release|bioassay
editor preferred term: cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120

RNA-seq assay
type: Class
subclass of: transcription profiling assay
subclass of: OBI_0600047
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      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: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400103
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
curator note: JZ: should be inferred as 'DNA sequencing'. Will check in the future.
definition: An assay 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
definition source: EFO_0002770 transcription profiling by high throughput sequencing
term editor: PERSON: James Malone
editor preferred term: RNA-seq assay
curator note: an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq
alternative term: transcription profiling by high throughput sequencing
has curation status: IAO_0000120

ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNF release|ELISPOT
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-5 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-5 production by T cells
definition: An assay of epitope specific interleukin-5 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-5 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120

genotyping by array assay
type: Class
subclass of: genotyping assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
term editor: Group: ArrayExpress production team
definition: An assay in which an array is used to detect polymorphisms in DNA samples
definition source: EFO_0002767: genotyping by array
editor preferred term: genotyping by array assay
has curation status: IAO_0000120

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
definition: A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-16 production by T cells
has curation status: IAO_0000122

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: chemokine (C-C motif) ligand 1 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells.
IEDB alternative term: CCL1/TCA-3 release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interleukin-2 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-2 production by T cells
definition: An assay of epitope specific interleukin-2 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-2 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

DNA methylation profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: DNA methylation profiling by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
subclass of: Restriction
  on property: has part
  some values from: epigenetic modification identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
editor preferred term: DNA methylation profiling by array design
definition source: GROUP: ArrayExpress production team
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interleukin-22 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-22 production by T cells
definition: An assay of epitope specific interleukin-22 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-22 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

biological activity assay measuring epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-16 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells.
definition source: IEDB
IEDB alternative term: IL-16 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-16 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific IP-10 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific IP-10 production by T cells
definition: An assay of epitope specific IP-10 production by T cells that uses an ELISA.
IEDB alternative term: CXCL10/IP-10 release|ELISA
editor preferred term: ELISA measuring epitope specific IP-10 production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

translation profiling assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
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.
definition source: EFO_0001033 translation profiling
term editor: PERSON: James Malone
editor preferred term: translation profiling assay
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-15 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-15 production by T cells
definition: An assay of epitope specific interleukin-15 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-15 production by T cells
definition source: IEDB
IEDB alternative term: IL-15 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-12 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-12 production by T cells
definition: An assay of epitope specific interleukin-12 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-12 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120

in vitro design
type: Class
subclass of: OBI_0500000
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_347 in_vitro_design
editor preferred term: in vitro design
has curation status: IAO_0000120

RNAi profiling by array design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: RNAi profiling by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: Group: ArrayExpress production team
editor preferred term: RNAi profiling by array design
has curation status: IAO_0000120

ELISA measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific lymphotoxin A production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: biological activity assay measuring epitope specific lymphotoxin A production by T cells
definition: An assay of epitope specific lymphotoxin A production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific lymphotoxin A production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: lymphotoxin A/TNFb release|ELISA
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-5 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-5 production by T cells
definition: An assay of epitope specific interleukin-5 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-5 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120

transcription profiling by array design
type: Class
subclass of: transcription profiling design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: transcription profiling by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
definition source: MO_533 transcript_identification_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
editor preferred term: transcription profiling by array design
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interleukin-17 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-17 production by T cells
definition: An assay of epitope specific interleukin-17 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-17 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

biological activity assay measuring epitope specific interleukin-15 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-15 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells.
definition source: IEDB
IEDB alternative term: IL-15 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-15 production by T cells
has curation status: IAO_0000120

disease state 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: OGMS_0000031
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_902 disease_state_design
editor preferred term: disease state design
has curation status: IAO_0000120

wild type organism genotype information
type: Class
subclass of: genotype information
example of usage: C57BL/6J wild type
term editor: Group: OBI group
definition source: Group: OBI group
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
editor preferred term: wild type organism genotype information
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-17 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells.
definition source: IEDB
IEDB alternative term: IL-17 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-17 production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-17 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-17 production by T cells
definition: An assay of epitope specific interleukin-17 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-17 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-10 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-10 production by T cells
definition: An assay of epitope specific interleukin-10 production by T cells that uses a cytometric bead array assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-10 release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interleukin-21 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-21 production by T cells
definition: An assay of epitope specific interleukin-21 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-21 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-5 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-5 production by T cells
definition: An assay of epitope specific interleukin-5 production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
IEDB alternative term: IL-5 release|ICS
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-2 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-2 production by T cells
definition: An assay of epitope specific interleukin-2 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-2 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-16 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-16 production by T cells
definition: An assay of epitope specific interleukin-16 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-16 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
definition: An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an ELISA.
IEDB alternative term: CCL3/MIP-1a release|ELISA
editor preferred term: ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an intracellular cytokine staining assay.
IEDB alternative term: GM-CSF release|ICS
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120

RNAi profiling by array assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
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.
definition source: EFO_0001030 RNAi profiling by array
term editor: PERSON: James Malone
editor preferred term: RNAi profiling by array assay
has curation status: IAO_0000120

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
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
term editor: Group: OBI group
definition source: Group: OBI group
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
editor preferred term: genotype information
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that examines the stability and/or decay of RNA transcripts.
definition source: MO_553 RNA_stability_design
editor preferred term: RNA stability design
has curation status: IAO_0000120

tiling microarray
type: Class
subclass of: OBI_0400148
definition source: EFO_0002704: tiling array
term editor: Person: Helen Parkinson
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.
alternative term: genome tiling array
editor preferred term: tiling microarray
has curation status: IAO_0000120

biological activity assay measuring epitope specific IP-10 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: IP-10 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects IP-10 production by T cells.
IEDB alternative term: CXCL10/IP-10 release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific IP-10 production by T cells
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-13 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-13 production by T cells
definition: An assay of epitope specific interleukin-13 production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
IEDB alternative term: IL-13 release|ICS
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120

species comparison 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: OBI_0100026
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
definition: A study design that assays differences between distinct species.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_675 species_design
editor preferred term: species comparison design
has curation status: IAO_0000120

X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: OBI_0001999
  intersection of: Restriction
    on property: has part
    some values from: X-ray crystallography assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000019
subclass of: OBI_0001999
IEDB alternative term: 3D structure|x-ray crystallography|angstroms
definition: A T cell epitope 3D structure determination assay that uses an X-ray crystallography assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
has curation status: IAO_0000120

transcription profiling by RT-PCR design
type: Class
subclass of: transcription profiling design
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: transcription profiling by RT-PCR assay
      intersection of: Restriction
        on property: has participant
        some values from: PCR instrument
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
definition source: Group: ArrayExpress production team
editor preferred term: transcription profiling by RT-PCR design
has curation status: IAO_0000120

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
definition: A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific T cell enhancement of B cell mediated immune response
has curation status: IAO_0000122

ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
definition: An assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells that uses an ELISA.
IEDB alternative term: CCL1/TCA-3 release|ELISA
editor preferred term: ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

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
definition: A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-21 production by T cells
has curation status: IAO_0000122

flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
type: Class
equivalent class: Class
  intersection of: OBI_1110124
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: fluorescence detection binding assay
subclass of: OBI_1110124
definition: A T cell epitope qualitative binding assay that uses a cell-cell binding detection by flow cytometry assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: T cell- APC binding|binding assay
editor preferred term: flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
has curation status: IAO_0000120

proteomic profiling by array assay
type: Class
subclass of: analyte assay
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400149
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      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
term editor: Person: James Malone
definition: An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
definition source: EFO_0002765 proteomic profiling by array
editor preferred term: proteomic profiling by array assay
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interferon-gamma production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interferon-gamma production by T cells
definition: An assay of epitope specific interferon-gamma production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IFNg release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120

ELISPOT assay measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granzyme B release by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific granzyme B release by T cells
definition: A T cell epitope specific granzyme B release assay that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific granzyme B release by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: granzyme B release|ELISPOT
has curation status: IAO_0000120

microRNA profiling by array design
type: Class
subclass of: transcription profiling design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: microRNA profiling by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
definition source: Group: ArrayExpress production team
editor preferred term: microRNA profiling by array design
has curation status: IAO_0000120

in vivo assay measuring T cell epitope specific tolerance induction
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring T cell epitope specific in vivo activity
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001983
  intersection 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: Class
subclass of: biological activity assay measuring T cell epitope specific in vivo activity
definition: An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: in vivo assay measuring T cell epitope specific tolerance induction
IEDB alternative term: tolerance|in vivo assay
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific RANTES production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific RANTES production by T cells
definition: An assay of epitope specific RANTES production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
IEDB alternative term: CCL5/RANTES release|RNA/DNA detection
definition source: IEDB
term editor: IEDB
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

cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-4 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-4 production by T cells
definition: An assay of epitope specific interleukin-4 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-4 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection 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: lymphotoxin A production
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific lymphotoxin A production by T cells
IEDB alternative term: lymphotoxin A/TNFb release|biological activity
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
definition source: MO_892 development_or_differentiation_design
editor preferred term: organism development design
has curation status: IAO_0000120

family history design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
definition source: MO_544 family_history_design
editor preferred term: family history design
has curation status: IAO_0000120

ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
definition: An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an ELISA.
IEDB alternative term: CXCL9/MIG release|ELISA
editor preferred term: ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
term editor: IEDB
definition source: IEDB
has curation status: IAO_0000120

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
definition: A molecular feature identification objective that aims to characterize the abundance of transcripts
definition source: Group: Penn Group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: transcription profiling identification objective
has curation status: IAO_0000120

DNA methylation profiling by array assay
type: Class
equivalent class: Class
  intersection of: DNA methylation profiling assay
  intersection of: Restriction
    on property: has participant
    some values from: OBI_0400148
subclass of: DNA methylation profiling assay
term editor: Person: James Malone
comment: Philippe Rocca-Serra
definition: An assay in which the methylation state of DNA is determined and is compared between samples using array technology
editor preferred term: DNA methylation profiling by array assay
definition source: EFO_0002759 methylation profiling by array
has curation status: IAO_0000120

biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: macrophage inflammatory protein-1 alpha production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells.
IEDB alternative term: CCL3/MIP-1a release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000120

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
definition: A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific granulocyte colony stimulating factor production by T cells
has curation status: IAO_0000122

microRNA profiling by array assay
type: Class
subclass of: OBI_0001926
subclass of: Restriction
  on property: has participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measured expression level
    intersection of: 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
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: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
definition: An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome.
definition source: EFO_0000753 microRNA profiling by array
term editor: PERSON: James Malone
editor preferred term: microRNA profiling by array assay
has curation status: IAO_0000120

quality control testing design
type: Class
subclass of: OBI_0500000
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
definition source: MO_981 quality_control_testing_design
editor preferred term: quality control testing design
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
definition source: MO_832 clinical_history_design
editor preferred term: clinical history design
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interleukin-4 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-4 production by T cells
definition: An assay of epitope specific interleukin-4 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-4 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cell culture analyte detection bioassay.
IEDB alternative term: GM-CSF release|bioassay
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-21 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-21 production by T cells
definition: An assay of epitope specific interleukin-21 production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
IEDB alternative term: IL-21 release|ICS
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
definition: An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
IEDB alternative term: CCL2/MCP-1 release|RNA/DNA detection
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
definition: An assay of epitope specific monocyte chemotactic protein-1 production by T cells that uses an ELISA.
IEDB alternative term: CCL2/MCP-1 release|ELISA
editor preferred term: ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: chemokine (C-C motif) ligand 4 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells.
IEDB alternative term: CCL4/MIP-1b release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-21 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-21 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-21 production by T cells
definition: An assay of epitope specific interleukin-21 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-21 production by T cells
definition source: IEDB
IEDB alternative term: IL-21 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring T cell epitope specific in vivo activity
  intersection 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: Class
subclass of: biological activity assay measuring T cell epitope specific in vivo activity
definition: An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
IEDB alternative term: type IV hypersensitivity (DTH)|in vivo skin test
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-13 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-13 production by T cells
definition: An assay of epitope specific interleukin-13 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-13 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interferon-gamma production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interferon-gamma production by T cells
definition: An assay of epitope specific interferon-gamma production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IFNg release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

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
definition: A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000122

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
definition source: MO_58 Allele
term editor: Person: Chris Stoeckert, Jie Zheng
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 preferred term: allele information
editor note: discussed on San Diego OBI workshop, March 2011
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
definition: A T cell epitope specific tumor necrosis factor production assay that uses a cytometric bead array assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNFa release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells
has curation status: IAO_0000120

ELISPOT assay measuring epitope specific interleukin-17 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-17 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific interleukin-17 production by T cells
definition: An assay of epitope specific interleukin-17 production by T cells that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific interleukin-17 production by T cells
definition source: IEDB
IEDB alternative term: IL-17 release|ELISPOT
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interferon-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interferon-beta production by T cells
definition: An assay of epitope specific interferon-beta production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IFNb release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

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: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
IEDB alternative term: GM-CSF release|RNA/DNA detection
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
definition source: MO_392 cellular_modification_design
comment: post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
editor preferred term: post-transcriptional modification design
has curation status: IAO_0000120

ELISA measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-8 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific interleukin-8 production by T cells
definition: An assay of epitope specific interleukin-8 production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific interleukin-8 production by T cells
definition source: IEDB
IEDB alternative term: IL-8 release|ELISA
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-6 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-6 production by T cells
definition: An assay of epitope specific interleukin-6 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-6 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120

transcription profiling by RT-PCR assay
type: Class
subclass of: transcription profiling assay
subclass of: Restriction
  on property: has participant
  some values from: PCR instrument
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: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: has part
  some values from: reverse transcribed polymerase chain reaction
definition: An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR)
definition source: EFO_0002943: transcription profiling by RT-PCR
term editor: Person: Anna Farne
editor preferred term: transcription profiling by RT-PCR assay
has curation status: IAO_0000120

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
definition: A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific chemokine (C-C motif) ligand 4 production by T cells
has curation status: IAO_0000122

biological activity assay measuring epitope specific interleukin-23 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-23 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells.
definition source: IEDB
IEDB alternative term: IL-23 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-23 production by T cells
has curation status: IAO_0000120

genetic alteration information
type: Class
subclass of: genetic characteristics information
term editor: Group: OBI group
definition source: Group: OBI group
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 preferred term: genetic alteration information
editor note: proposed and discussed on San Diego OBI workshop, March 2011
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_810 cellular_process_design
editor preferred term: cellular process design
has curation status: IAO_0000120

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
definition: A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific RANTES production by T cells
has curation status: IAO_0000122

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: biological activity assay measuring epitope specific interleukin-10 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-10 production by T cells
definition: An assay of epitope specific interleukin-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-10 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNF release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120

wild type allele information
type: Class
subclass of: allele information
definition source: MO_605 genotype
term editor: Person: Chris Stoeckert, Jie Zheng
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
editor preferred term: wild type allele information
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
definition: An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an intracellular cytokine staining assay.
IEDB alternative term: CCL4/MIP-1b release|ICS
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

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
definition: A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific granzyme B production by T cells
has curation status: IAO_0000122

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
definition: A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-8 production by T cells
has curation status: IAO_0000122

injury design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the response of an organism(s) to injury or damage is studied.
definition source: MO_726 injury_design
editor preferred term: injury design
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-3 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-3 production by T cells
definition: An assay of epitope specific interleukin-3 production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
IEDB alternative term: IL-3 release|ICS
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120

organism status comparison design
type: Class
subclass of: OBI_0500000
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
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that compares samples from live and dead organisms.
definition source: MO_841 organism_status_design
editor preferred term: organism status comparison design
has curation status: IAO_0000120

ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
definition: An assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells that uses an ELISA.
IEDB alternative term: CCL4/MIP-1b release|ELISA
editor preferred term: ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interferon-gamma production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interferon-gamma production by T cells
definition: An assay of epitope specific interferon-gamma production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IFNg release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-18 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-18 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells.
definition source: IEDB
IEDB alternative term: IL-18 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-18 production by T cells
has curation status: IAO_0000120

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
definition: A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-23 production by T cells
has curation status: IAO_0000122

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: biological activity assay measuring epitope specific interleukin-27 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-27 production by T cells
definition: An assay of epitope specific interleukin-27 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-27 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

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: biological activity assay measuring epitope specific IP-10 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific IP-10 production by T cells
definition: An assay of epitope specific IP-10 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
IEDB alternative term: CXCL10/IP-10 release|RNA/DNA detection
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-3 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-3 production by T cells
definition: An assay of epitope specific interleukin-3 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-3 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNF release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120

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
definition: A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000122

genotyping by array design
type: Class
subclass of: genotyping design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: genotyping by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
definition source: MO_560 genotyping_design
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
editor preferred term: genotyping by array design
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-1 alpha production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells.
definition source: IEDB
IEDB alternative term: IL-1a release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-1 alpha production by T cells
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific interleukin-6 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-6 production by T cells
definition: An assay of epitope specific interleukin-6 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-6 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

biological activity assay measuring epitope specific interferon-beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interferon-beta production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells.
definition source: IEDB
IEDB alternative term: IFNb release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interferon-beta production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-12 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells.
definition source: IEDB
IEDB alternative term: IL-12 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120

in vivo assay measuring epitope specific T cell killing
type: Class
equivalent class: Class
  intersection of: OBI_1110130
  intersection of: Restriction
    on property: has part
    some values from: in vivo cell killing assay
subclass of: OBI_1110130
definition: A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: cytotoxicity|in vivo assay
editor preferred term: in vivo assay measuring epitope specific T cell killing
has curation status: IAO_0000120

comparative genomic hybridization by array assay
type: Class
subclass of: genotyping assay
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 participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: molecular feature identification objective
subclass of: Restriction
  on property: has_specified_output
  some values from: genotype information
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: deoxyribonucleic acid
comment: Philippe Rocca-Serra
definition: An assay in which changes in DNA sequence copy number are analysed 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.
definition source: EFO_0000749: comparative genomic hybridization by array
term editor: Person: James Malone
alternative term: array CGH
editor preferred term: comparative genomic hybridization by array assay
has curation status: IAO_0000120

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
definition: A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific cytotoxic T cell degranulation
has curation status: IAO_0000122

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: biological activity assay measuring epitope specific interleukin-23 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-23 production by T cells
definition: An assay of epitope specific interleukin-23 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
IEDB alternative term: IL-23 release|RNA/DNA detection
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

stimulus or stress 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: organism feature identification objective
    intersection of: Restriction
      on property: is about
      some values from: response to stimulus
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_568 stimulus_or_stress_design
editor preferred term: stimulus or stress design
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses a cytometric bead array assay.
IEDB alternative term: G-CSF release|cytometric bead array
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
has curation status: IAO_0000120

protein and DNA interaction identification objective
type: Class
subclass of: sequence feature identification objective
definition: A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
definition source: MO_933 binding_site_identification_design
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: protein and DNA interaction identification objective
has curation status: IAO_0000120

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
definition: A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-22 production by T cells
has curation status: IAO_0000122

biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: tumor necrosis factor superfamily cytokine production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNF release|biological activity
editor preferred term: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
has curation status: IAO_0000120

protocol optimization design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: protocol optimization objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
definition source: MO_934 optimization_design
editor preferred term: protocol optimization design
has curation status: IAO_0000120

promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-2 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: promoter activity detection by reporter gene assay
subclass of: biological activity assay measuring epitope specific interleukin-2 production by T cells
definition: An assay of epitope specific interleukin-2 production by T cells that uses a promoter activity detection by reporter gene assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-2 release|reporter gene assay
editor preferred term: promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120

ChIP-chip design
type: Class
subclass of: protein binding site identification design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: ChIP-chip assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400148
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
alternative term: ChIP-on-chip design
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.
editor preferred term: ChIP-chip design
definition source: MO_933 binding_site_identification_design
term editor: Person: Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120

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: inheres in
        some values from: Class
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)
definition source: MO_66 IndividualGeneticCharacteristics
term editor: Person: Chris Stoeckert, Jie Zheng
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
editor preferred term: genetic characteristics information
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
definition: An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses a cytometric bead array assay.
IEDB alternative term: CCL3/MIP-1a release|cytometric bead array
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-3 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-3 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells.
definition source: IEDB
IEDB alternative term: IL-3 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-3 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific T cell activation
type: Class
subclass of: OBI_0002055
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
editor preferred term: biological activity assay measuring epitope specific T cell activation
has curation status: IAO_0000120

imprinting design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_914 imprinting_design
editor preferred term: imprinting design
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_822 cell_cycle_design
editor preferred term: cell cycle design
has curation status: IAO_0000120

translation profiling design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Restriction
      on property: has part
      some values from: translation profiling assay
subclass of: Restriction
  on property: has part
  some values from: molecular feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: Group: ArrayExpress production team
editor preferred term: translation profiling design
has curation status: IAO_0000120

cell type comparison 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: cell
subclass of: Restriction
  on property: has part
  some values from: cellular feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that compares cells of different type, for example different cell lines.
definition source: MO_764 cell_type_comparison_design
editor preferred term: cell type comparison design
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific RANTES production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific RANTES production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific RANTES production by T cells
definition: An assay of epitope specific RANTES production by T cells that uses a cytometric bead array assay.
IEDB alternative term: CCL5/RANTES release|cytometric bead array
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific RANTES production by T cells
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-6 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific interleukin-6 production by T cells
definition: An assay of epitope specific interleukin-6 production by T cells that uses a cell culture analyte detection bioassay.
definition source: IEDB
IEDB alternative term: IL-6 release|bioassay
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interferon-gamma production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells.
definition source: IEDB
IEDB alternative term: IFNg release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120

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
definition: A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-9 production by T cells
has curation status: IAO_0000122

biological activity assay measuring epitope specific tumor necrosis factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection 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: tumor necrosis factor production
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNFa release|biological activity
editor preferred term: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
has curation status: IAO_0000120

ChIP-chip by tiling array design
type: Class
subclass of: ChIP-chip design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    all values from: Class
      intersection of: Restriction
        on property: has part
        some values from: ChIP-chip by tiling array assay
      intersection of: Restriction
        on property: has participant
        some values from: tiling microarray
definition source: Group: ArrayExpress production team
term editor: Person: Chris Stoeckert, Jie Zheng
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.
editor preferred term: ChIP-chip by tiling array design
has curation status: IAO_0000120

dose response design
type: Class
subclass of: compound treatment 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: dose specification
        intersection of: Restriction
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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that examines the relationship between the size of the administered dose and the extent of the response.
definition source: MO_485 dose_response_design
editor preferred term: dose response design
has curation status: IAO_0000120

ChIP-chip by tiling array assay
type: Class
subclass of: ChIP-chip assay
subclass of: Restriction
  on property: has participant
  some values from: tiling microarray
term editor: Group: ArrayExpress production team
definition: An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology
editor preferred term: ChIP-chip by tiling array assay
definition source: EFO_0002762 ChIP-chip by tiling array
has curation status: IAO_0000120

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
definition: A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific helper T cell enhancement of T cell mediated immune response
has curation status: IAO_0000122

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
definition: A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interferon-beta production by T cells
has curation status: IAO_0000122

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
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
editor preferred term: organism part comparison design
has curation status: IAO_0000120

intracellular material detection measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granzyme B release by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific granzyme B release by T cells
definition: A T cell epitope specific granzyme B release assay that uses an intracellular material detection by flow cytometry assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: granzyme B release|intracellular staining
editor preferred term: intracellular material detection measuring epitope specific granzyme B release by T cells
has curation status: IAO_0000120

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
definition: A study design that investigates protein binding sites on nucleic acids.
definition source: MO_933 binding_site_identification_design
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: protein binding site identification design
has curation status: IAO_0000120

sex comparison 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: PATO_0000047
subclass of: Restriction
  on property: has part
  some values from: organism feature identification objective
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
editor preferred term: sex comparison design
has curation status: IAO_0000120

transcription profiling by tiling array design
type: Class
subclass of: transcription profiling design
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: transcription profiling by tiling array assay
      intersection of: Restriction
        on property: has participant
        some values from: tiling microarray
subclass of: Restriction
  on property: has part
  some values from: transcription profiling identification objective
definition source: MO_507 tiling_path_design
term editor: Person: Chris Stoeckert, Jie Zheng
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.
editor preferred term: transcription profiling by tiling array design
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that assays events associated with cell development or differentiation.
definition source: MO_892 development_or_differentiation_design
editor preferred term: cell differentiation design
has curation status: IAO_0000120

transcription profiling design
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: transcription profiling identification objective
  intersection of: Restriction
    on property: is concretized as
    some values from: Restriction
      on property: realized in
      some values from: Restriction
        on property: has part
        some values from: transcription profiling assay
subclass of: OBI_0500000
definition: A study design that identifies forms and abundance of transcripts in the genome.
definition source: MO_533 transcript_identification_design
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: transcription profiling design
has curation status: IAO_0000120

operon identification design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: sequence feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that identifies locations and members of operons in a genome.
definition source: MO_772 operon_identification_design
editor preferred term: operon identification design
has curation status: IAO_0000120

radio immuno assay measuring epitope specific interferon-gamma production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interferon-gamma production by T cells
  intersection of: Restriction
    on property: has part
    some values from: radio immuno assay
subclass of: biological activity assay measuring epitope specific interferon-gamma production by T cells
definition: An assay of epitope specific interferon-gamma production by T cells that uses a radio immuno assay.
definition source: IEDB
IEDB alternative term: IFNg release|radio immuno assay (RIA)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: radio immuno assay measuring epitope specific interferon-gamma production by T cells
has curation status: IAO_0000120

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
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: DNA methylation profiling by high throughput sequencing assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400103
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
editor preferred term: DNA methylation profiling by high throughput sequencing design
definition source: GROUP: ArrayExpress production team
has curation status: IAO_0000120

biological activity assay measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific cytotoxic T cell degranulation
  intersection 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: granzyme B production
subclass of: biological activity assay measuring epitope specific cytotoxic T cell degranulation
definition: A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific granzyme B release by T cells
IEDB alternative term: granzyme B release|biological activity
has curation status: IAO_0000120

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: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
definition: An assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells that uses an intracellular cytokine staining assay.
IEDB alternative term: CXCL9/MIG release|ICS
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
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

ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
definition: An assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells that uses an ELISA.
IEDB alternative term: CCL9/MIP-1g release|ELISA
editor preferred term: ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

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
definition: A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
has curation status: IAO_0000122

all pairs design
type: Class
subclass of: OBI_0500000
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which all specimens are compared to every other specimen.
definition source: MO_565 all_pairs
editor preferred term: all pairs design
has curation status: IAO_0000120

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
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: proteomic profiling by array assay
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0400149
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
definition source: Group: ArrayExpress production team
editor preferred term: proteomic profiling by array design
has curation status: IAO_0000120

q-value
type: Class
subclass of: quantitative confidence 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)"
editor preferred term: q-value
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.
definition source: Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
alternative term: FDR adjusted p-value
term editor: PERS:Philippe Rocca-Serra
has curation status: IAO_0000122

genotyping design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: sequence feature identification objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Restriction
      on property: has part
      some values from: genotyping assay
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
definition source: MO_560 genotyping_design
editor preferred term: genotyping design
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-2 production by T cells
type: Class
subclass of: OBI_1110129
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: interleukin-2 production
definition: A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells.
definition source: IEDB
IEDB alternative term: IL-2 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-2 production by T cells
has curation status: IAO_0000120

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
definition: A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-15 production by T cells
has curation status: IAO_0000122

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
definition: A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific macrophage inflammatory protein-1 gamma production by T cells
has curation status: IAO_0000122

individual genetic characteristics comparison 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: genetic characteristics information
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design where genotype, haplotype, or other individual genetic characteristics are compared.
definition source: MO_527 individual_genetic_characteristics_design
editor preferred term: individual genetic characteristics comparison design
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-1 beta production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-1 beta production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells.
definition source: IEDB
IEDB alternative term: IL-1b release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-1 beta production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-4 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-4 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells.
definition source: IEDB
IEDB alternative term: IL-4 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-4 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-6 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-6 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells.
definition source: IEDB
IEDB alternative term: IL-6 release|biological activity
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific interleukin-6 production by T cells
has curation status: IAO_0000120

cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: reporter cell line analyte detection bioassay
subclass of: biological activity assay measuring epitope specific tumor necrosis factor production by T cells
definition: A T cell epitope specific tumor necrosis factor production assay that uses a cell culture analyte detection bioassay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNFa release|bioassay
editor preferred term: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific lymphotoxin A production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity 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
definition: An assay of epitope specific lymphotoxin A production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
IEDB alternative term: lymphotoxin A/TNFb release|ICS
has curation status: IAO_0000120

pathogenicity design
type: Class
subclass of: OBI_0500000
subclass of: Restriction
  on property: has part
  some values from: biological feature identification objective
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_807 pathogenicity_design
editor preferred term: pathogenicity design
has curation status: IAO_0000120

ELISPOT assay measuring epitope specific interleukin-5 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-5 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: OBI_0600031
subclass of: biological activity assay measuring epitope specific interleukin-5 production by T cells
definition: An assay of epitope specific interleukin-5 production by T cells that uses an ELISPOT assay.
editor preferred term: ELISPOT assay measuring epitope specific interleukin-5 production by T cells
definition source: IEDB
IEDB alternative term: IL-5 release|ELISPOT
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: macrophage inflammatory protein-1 gamma production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells.
IEDB alternative term: CCL9/MIP-1g release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-8 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-8 production by T cells
definition: An assay of epitope specific interleukin-8 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
IEDB alternative term: IL-8 release|cytometric bead array
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: chemokine (C-X-C motif) ligand 9 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells.
IEDB alternative term: CXCL9/MIG release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
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.
definition source: MO_447 genetic_modification_design
editor preferred term: genetic modification design
has curation status: IAO_0000120

ELISA measuring epitope specific granzyme B release by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granzyme B release by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific granzyme B release by T cells
definition: A T cell epitope specific granzyme B release assay that uses an ELISA.
editor preferred term: ELISA measuring epitope specific granzyme B release by T cells
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: granzyme B release|ELISA
has curation status: IAO_0000120

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
definition: A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific IP-10 production by T cells
has curation status: IAO_0000122

transcription profiling by array assay
type: Class
subclass of: transcription profiling assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
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 participant
  some values from: OBI_0400148
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
definition: An assay in which the transcriptome of a biological sample is analysed using array technology.
term editor: Person: James Malone
definition source: EFO_0002768: transcription profiling by array
alternative term: RNA profiling by array assay
editor note: JZ: add alternative term: 'RNA profiling by array assay' requested by ENCODE developer. See tracker: https://sourceforge.net/p/obi/obi-terms/757/
editor preferred term: transcription profiling by array assay
has curation status: IAO_0000120

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
term editor: Person: Chris Stoeckert, Jie Zheng
definition: A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
definition source: MO_462 strain_or_line_design
editor preferred term: strain comparison design
has curation status: IAO_0000120

biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: monocyte chemotactic protein-1 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells.
IEDB alternative term: CCL2/MCP-1 release|biological activity
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-12 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-12 production by T cells
definition: An assay of epitope specific interleukin-12 production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
IEDB alternative term: IL-12 release|ICS
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
has curation status: IAO_0000120

in vivo assay measuring T cell epitope specific disease exacerbation
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring T cell epitope specific in vivo activity
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001981
subclass of: biological activity assay measuring T cell epitope specific in vivo activity
definition: An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment.
definition source: IEDB
term editor: IEDB
IEDB alternative term: disease exacerbation|in vivo assay
editor preferred term: in vivo assay measuring T cell epitope specific disease exacerbation
has curation status: IAO_0000120

cell specimen
type: Class
subclass of: OBI_0100051
subclass of: Restriction
  on property: has part
  some values from: cell
subclass of: Restriction
  on property: has role
  some values from: specimen role
definition: A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
definition source: MO_612 cell
term editor: PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
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/
editor preferred term: cell specimen
has curation status: IAO_0000123

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: OBI_1110037
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.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: ligand presentation|T cell recognition
editor preferred term: monospecific T cell recognition assay measuring MHC ligand processing and presentation
has curation status: IAO_0000120

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
definition: A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-17F production by T cells
has curation status: IAO_0000122

T cell epitope specific immune intervention
type: Class
subclass of: epitope specific immune intervention
definition: An epitope specific immune intervention in which the induced response targets a T cell epitope
definition source: IEDB
example of usage: Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
term editor: PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: T cell epitope specific immune intervention
has curation status: IAO_0000120

specimen with known storage state
type: Class
equivalent class: 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
definition: A specimen for which it is known whether it has been subjected to storage of a specified type.
definition source: MO_95 BiosourceType
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: specimen with known storage state
has curation status: IAO_0000123

in vivo assay measuring T cell epitope specific protection from tumor challenge
type: Class
equivalent class: Class
  intersection of: OBI_0002073
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001982
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0001906
subclass of: OBI_0002073
definition: A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on tumor burden.
definition source: IEDB
term editor: IEDB
editor preferred term: in vivo assay measuring T cell epitope specific protection from tumor challenge
IEDB alternative term: tumor burden after challenge|in vivo assay
has curation status: IAO_0000120

lowess group transformation
type: Class
subclass of: lowess transformation
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.
definition source: MO_861 lowess_group_normalization
term editor: Person: Elisabetta Manduchi
editor preferred term: lowess group transformation
has curation status: IAO_0000120

in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
type: Class
equivalent class: Class
  intersection of: OBI_0002073
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001982
  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: pathogen role
subclass of: OBI_0002073
definition: A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on pathogen burden.
definition source: IEDB
term editor: IEDB
editor preferred term: in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
IEDB alternative term: pathogen burden after challenge|in vivo assay
has curation status: IAO_0000120

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: OBI_0600047
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_1000029
subclass of: binding assay
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.
definition source: IEDB
term editor: IEDB
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.
editor preferred term: phage display binding assay
has curation status: IAO_0000120

lowess transformation
type: Class
subclass of: OBI_0200169
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: OBI_0200167
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.
definition source: MO_720 lowess_normalization
term editor: Person: Elisabetta Manduchi
editor preferred term: lowess transformation
has curation status: IAO_0000120

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: mass spectrometry assay
subclass of: OBI_1110125
definition: A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands
definition source: IEDB
term editor: IEDB
IEDB alternative term: ligand presentation|mass spectrometry
editor preferred term: mass spectrometry assay measuring MHC ligand processing and presentation
has curation status: IAO_0000120

specimen from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: Class
      union of: UBERON_0000465
      union of: UBERON_0000477
subclass of: OBI_0100051
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).
definition source: MO_954 organism_part
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: specimen from organism
alternative term: tissue specimen
has curation status: IAO_0000122

phage display library panning
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: OBI_1000029
definition source: IEDB, http://en.wikipedia.org/wiki/Phage_display
term editor: Jason Greenbaum, Randi Vita, Bjoern Peters
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.
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.
editor preferred term: phage display library panning
has curation status: IAO_0000120

lowess global transformation
type: Class
subclass of: lowess transformation
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.
definition source: MO_692 lowess_global_normalization
term editor: Person: Elisabetta Manduchi
editor preferred term: lowess global transformation
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
definition: An assay of epitope specifictransforming growth factor-beta production by T cells that uses an intracellular cytokine staining assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: TGFb release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
has curation status: IAO_0000120

cell collecting
type: Class
subclass of: OBI_0600014
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
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
definition: A planned process that collects cells from culture.
definition source: MO_982 harvest
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: cell collecting
has curation status: IAO_0000120

biological activity assay measuring T cell epitope specific in vivo activity
type: Class
equivalent class: Class
  intersection of: OBI_0002055
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001980
  intersection of: Restriction
    on property: has_specified_input
    some values from: OBI_0100026
subclass of: OBI_0002055
definition: A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment.
definition source: IEDB
term editor: IEDB
editor preferred term: biological activity assay measuring T cell epitope specific in vivo activity
IEDB alternative term: in vivo activity|biological activity
has curation status: IAO_0000120

purified MHC molecule preparation
type: Class
subclass of: purified material
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
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
example of usage: HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody
editor preferred term: purified MHC molecule preparation
has curation status: IAO_0000120

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
definition source: IEDB
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.
alternative term: MHC ligand disposition
term editor: PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
editor preferred term: disposition to be bound by an MHC protein complex
has curation status: IAO_0000120

B cell epitope specific immune intervention
type: Class
subclass of: epitope specific immune intervention
definition: An epitope specific immune intervention in which the induced response targets a B cell epitope
editor preferred term: B cell epitope specific immune intervention
definition source: IEDB
example of usage: Injecting a mouse with recombinant antibody targeting an anthrax epitope
term editor: PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
has curation status: IAO_0000120

epitope tolerance induction experiment
type: Class
subclass of: efficacy of epitope intervention experiment
definition: An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
definition source: IEDB
term editor: IEDB
editor preferred term: epitope tolerance induction experiment
IEDB alternative term: tolerance induction
has curation status: IAO_0000120

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: mass spectrometry assay
definition: A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC.
definition source: IEDB
term editor: IEDB
IEDB alternative term: ligand presentation|cellular MHC/mass spectrometry
editor preferred term: mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC
has curation status: IAO_0000120

cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses a cytometric bead array assay.
IEDB alternative term: GM-CSF release|cytometric bead array
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
has curation status: IAO_0000120

radioactivity detection binding assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has part
    some values from: radioactivity detection
subclass of: binding assay
definition source: IEDB
term editor: PERSON:Bjoern Peters, Randi Vita
definition: binding assay that uses radioactivity detection as an indicator of binding
editor preferred term: radioactivity detection binding assay
has curation status: IAO_0000120

in vivo assay measuring T cell epitope specific protection based on survival
type: Class
equivalent class: Class
  intersection of: OBI_0002073
  intersection of: Restriction
    on property: has part
    some values from: epitope protection experiment based on survival
subclass of: OBI_0002073
definition: A T cell epitope in vivo intervention experiment that uses a protection from challenge in vivo intervention experiment based on survival.
term editor: IEDB
definition source: IEDB
editor preferred term: in vivo assay measuring T cell epitope specific protection based on survival
IEDB alternative term: survival from challenge|in vivo assay
has curation status: IAO_0000120

cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
type: Class
subclass of: cell bound MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: OBI_1110037
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
definition: A cell bound MHC binding assay that uses a T cell epitope recognition assay.
definition source: IEDB
term editor: IEDB
editor preferred term: cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
IEDB alternative term: qualitative binding|cellular MHC/T cell inhibition
has curation status: IAO_0000120

linear amplification
type: Class
subclass of: OBI_0600058
definition: An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
example of usage: An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
definition source: MO_997 linear_amplification
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: linear amplification
has curation status: IAO_0000120

biological activity assay measuring epitope specific T cell helper activity
type: Class
equivalent class: Class
  intersection of: OBI_0002055
  intersection 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: helper T cell enhancement of adaptive immune response
  intersection 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: Class
subclass of: OBI_0002055
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.
definition source: IEDB
term editor: IEDB
editor preferred term: biological activity assay measuring epitope specific T cell helper activity
IEDB alternative term: helper response|biological activity
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-22 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-22 production by T cells
definition: An assay of epitope specific interleukin-22 production by T cells that uses an intracellular cytokine staining assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-22 release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
has curation status: IAO_0000120

biological activity assay measuring epitope specific perforin release by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific cytotoxic T cell degranulation
  intersection 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: perforin production
subclass of: biological activity assay measuring epitope specific cytotoxic T cell degranulation
definition: A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells.
definition source: IEDB
term editor: IEDB
editor preferred term: biological activity assay measuring epitope specific perforin release by T cells
IEDB alternative term: perforin release|biological activity
has curation status: IAO_0000120

atmosphere
type: Class
subclass of: growth environment
definition: A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
definition source: MO_219 atmosphere
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: atmosphere
has curation status: IAO_0000120

fluorescence detection binding assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
subclass of: binding assay
definition source: IEDB
term editor: PERSON:Bjoern Peters, Randi Vita
definition: binding assay that uses fluorescence detection as an indicator of binding
editor preferred term: fluorescence detection binding assay
has curation status: IAO_0000120

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_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: positive reference substance role
subclass of: Restriction
  on property: has part
  some values from: OBI_1110037
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.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand
IEDB alternative term: ligand presentation|coelution
has curation status: IAO_0000120

fluorescence detection assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: PATO_0000018
    intersection of: Restriction
      on property: has_specified_input
      some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: PATO_0000018
subclass of: assay
definition: An assay in which a material's fluorescence is determined.
term editor: IEDB
definition source: IEDB
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.
editor preferred term: fluorescence detection assay
has curation status: IAO_0000120

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
term editor: PERSON: Bjoern Peters, Randi Vita
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
definition: The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
editor preferred term: epitope specific perforin production by T cells
has curation status: IAO_0000120

MHC protein complex binding to ligand
type: Class
subclass of: binding
subclass of: Class
  intersection of: binding
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: disposition
      intersection of: Restriction
        on property: inheres in
        some values from: Class
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.
definition source: IEDB
editor preferred term: MHC protein complex binding to ligand
term editor: PERSON: Bjoern Peters; Randi Vita
example of usage: The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
definition: The process in which a ligand binds to an MHC molecule to form a stable complex
has curation status: IAO_0000120

dissection
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
definition: A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
definition source: EFO_0003856 dissection
definition source: MO_374 dissect
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: dissection
has curation status: IAO_0000120

purification
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: purification objective
subclass of: OBI_0600014
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
definition source: MO_406 purify
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor preferred term: purification
has curation status: IAO_0000120

specimen with pre- or post-mortem status
type: Class
equivalent class: 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
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: OBI_0100051
definition: A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
definition source: MO_84 OrganismStatus
term editor: PERSON: Chris Stoeckert, Jie Zheng
editor note: organizational term, used in description of specimen that is created from known pre- or post-mortem status
editor preferred term: specimen with pre- or post-mortem status
has curation status: IAO_0000120

in vivo assay measuring T cell epitope specific treatment of disease
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring T cell epitope specific in vivo activity
  intersection of: Restriction
    on property: has part
    some values from: OBI_0001984
subclass of: biological activity assay measuring T cell epitope specific in vivo activity
definition: An efficacy of T cell epitope intervention experiment that detects a decrease in disease.
definition source: IEDB
term editor: IEDB
IEDB alternative term: decreased disease|in vivo assay
editor preferred term: in vivo assay measuring T cell epitope specific treatment of disease
has curation status: IAO_0000120

sampling time measurement datum
type: Class
subclass of: time measurement datum
definition: A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
definition source: MO_738 timepoint
term editor: Person: Chris Stoeckert
editor preferred term: sampling time measurement datum
alternative term: time point
has curation status: IAO_0000120

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: Edman degradation
subclass of: OBI_1110125
definition: A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands
editor preferred term: Edman degradation assay measuring MHC ligand processing and presentation
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: ligand presentation|Edman degradation
has curation status: IAO_0000120

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: mass spectrometry assay
definition: A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC.
definition source: IEDB
term editor: IEDB
IEDB alternative term: ligand presentation|secreted MHC/mass spectrometry
editor preferred term: mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC
has curation status: IAO_0000120

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
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.
definition source: IEDB
term editor: IEDB
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.
editor preferred term: disposition to be a product of antigen processing and presentation
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0001773
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
subclass of: OBI_0001773
definition: A T cell epitope specific interleukin-17A production assay that uses a cytometric bead array assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-17A release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
has curation status: IAO_0000120

purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
type: Class
subclass of: radioactivity detection binding assay
subclass of: purified MHC binding assay measuring binding of a MHC:ligand complex
subclass of: Restriction
  on property: has part
  some values from: radioactivity detection
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_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: OBI_0001955
definition: A purified MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
IEDB alternative term: qualitative binding|purified MHC/competitive/radioactivity
has curation status: IAO_0000120

minimal inhibitory concentration
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is about
  some values from: dose response curve
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
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.
definition source: Bjoern Peters, coordinated with Albert Goldfain
editor note: Created following request by Albert Goldfain
term editor: PERSON:Bjoern Peters
editor preferred term: minimal inhibitory concentration
has curation status: IAO_0000120

material maintenance service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: material maintenance
subclass of: material service
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.
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.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
editor preferred term: material maintenance service
example of usage: model organism colony maintanance
has curation status: IAO_0000125

cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001991
  intersection of: Restriction
    on property: has part
    some values from: 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: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: radioactivity detection binding assay
subclass of: OBI_0001991
definition: A cell lysate MHC ligand binding half maximal effective concentration (EC50) determination assay that uses radioactivity detection to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection
IEDB alternative term: half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM
has curation status: IAO_0000120

cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001992
  intersection of: Restriction
    on property: has part
    some values from: 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: radioactivity detection binding assay
subclass of: OBI_0001992
definition: A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
IEDB alternative term: half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM
has curation status: IAO_0000120

epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
type: Class
equivalent class: Class
  intersection of: tumor necrosis factor (ligand) superfamily member 11 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: tumor necrosis factor (ligand) superfamily member 11 production
subclass of: epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
has curation status: IAO_0000122

cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: cell lysate MHC binding assay measuring binding of a MHC:ligand complex
subclass of: Restriction
  on property: has part
  some values from: fluorescence detection assay
subclass 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
definition: A cell lysate MHC binding assay that uses fluorescence detection to detect direct binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection
IEDB alternative term: qualitative binding|lysate MHC/direct/fluorescence
has curation status: IAO_0000120

cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001992
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: fluorescence detection binding assay
subclass of: OBI_0001992
definition: A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
IEDB alternative term: half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM
has curation status: IAO_0000120

ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
definition: An assay of epitope specific granulocyte colony stimulating factor production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells
IEDB alternative term: G-CSF release|ELISA
definition source: IEDB
term editor: IEDB
has curation status: IAO_0000120

sequence assembly algorithm
type: Class
subclass of: algorithm
definition: An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured.
Source: NIAID GSCID-BRC
NIAID GSCID-BRC alternative term: Assembly Algorithm
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: sequence assembly algorithm
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-17F production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0001772
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
subclass of: OBI_0001772
definition: A T cell epitope specific interleukin-17F production assay that uses a cytometric bead array assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-17F release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-17F production by T cells
has curation status: IAO_0000120

cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001987
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000285
subclass of: fluorescence detection binding assay
subclass of: OBI_0001987
definition: A cell bound MHC ligand binding equilibrium association constant (KA) determination assay that uses fluorescence detection to detect direct binding.
definition source: IEDB
term editor: IEDB
IEDB alternative term: association constant KA|cellular MHC/direct/fluorescence|1/M
editor preferred term: cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

PDB file
type: Class
subclass of: 3D structural organization datum
definition: A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned.
editor preferred term: PDB file
term editor: PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
example of usage: The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
has curation status: IAO_0000120

epitope specific interleukin-17A production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-17A production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-17A production
subclass of: OBI_1110193
definition: A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-17A production by T cells
has curation status: IAO_0000122

support service
type: Class
subclass of: service
definition: A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data.
example of usage: An help desk for an instrument or a software.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON; Carlo Torniai
editor preferred term: support service
has curation status: IAO_0000125

material service
type: Class
equivalent class: Class
  intersection of: service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: Class
      union of: Restriction
        on property: has_specified_input
        some values from: material entity
      union of: Restriction
        on property: has_specified_output
        some values from: material entity
subclass of: service
example of usage: A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
definition: A service which has a material entity as specified input and/or specified output.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
editor preferred term: material service
has curation status: IAO_0000125

data analysis service
type: Class
subclass of: data service
subclass of: Restriction
  on property: has part
  some values from: OBI_0200000
definition: A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
example of usage: Statistaical analysis service, data visualization service
editor preferred term: data analysis service
has curation status: IAO_0000125

data service
type: Class
subclass of: service
subclass of: Restriction
  on property: has_specified_output
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
definition: A service that has some information content entity as input and output.
example of usage: Data analysis service such statistical abalysis or storage service such data backup.
comment: Information content entity was used as specified input and output since it was more appropriate then data item or dataset.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
editor preferred term: data service
has curation status: IAO_0000125

purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001990
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  intersection 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000031
subclass of: fluorescence detection binding assay
subclass of: OBI_0001990
definition: A purified MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding.
definition source: IEDB
term editor: IEDB
IEDB alternative term: half life|purified MHC/direct/fluorescence|min
editor preferred term: purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-9 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring interleukin-9 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring interleukin-9 production by T cells
definition: An assay of epitope specific interleukin-9 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-9 release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-9 production by T cells
has curation status: IAO_0000120

data storage service
type: Class
subclass of: data service
example of usage: A service offering data backup
definition: A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
editor preferred term: data storage service
has curation status: IAO_0000125

purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: purified MHC binding assay measuring binding of a MHC:ligand complex
subclass of: Restriction
  on property: has part
  some values from: 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 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
definition: A purified MHC binding assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
term editor: IEDB
definition source: IEDB
editor preferred term: purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection
IEDB alternative term: qualitative binding|purified MHC/competitive/fluorescence
has curation status: IAO_0000120

epitope specific interleukin-7 production by T cells
type: Class
equivalent class: Class
  intersection of: interleukin-7 production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: interleukin-7 production
subclass of: epitope specific cytokine production by T cells
definition: A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific interleukin-7 production by T cells
has curation status: IAO_0000122

equilibrium dissociation constant (KD)
type: Class
subclass of: binding constant
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000051
definition: A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
definition source: IEDB
example of usage: KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
term editor: PERSON: Bjoern Peters, Randi Vita
editor preferred term: equilibrium dissociation constant (KD)
has curation status: IAO_0000120

purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001988
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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: purified MHC molecule preparation
      intersection of: Restriction
        on property: has part
        some values from: MHC protein complex
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: fluorescence detection binding assay
subclass of: OBI_0001988
definition: A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: dissociation constant KD|purified MHC/competitive/fluorescence|nM
editor preferred term: purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

training service
type: Class
subclass of: service
subclass of: Restriction
  on property: has part
  some values from: training process
definition: A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer.
example of usage: A service that offers training for a specific instrument or technique. A course to learn how to use a microscope
term editor: PERSON: Carlo Torniai
definition source: PERSON: Matthew Brush
term editor: PERSON: Matthew Brush
editor preferred term: training service
has curation status: IAO_0000125

cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001988
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: fluorescence detection binding assay
subclass of: OBI_0001988
definition: A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: IEDB
editor preferred term: cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
IEDB alternative term: dissociation constant KD|cellular MHC/competitive/fluorescence|nM
has curation status: IAO_0000120

obsolete T cell recognition of eluted MHC ligand assay
type: Class
subclass of: ObsoleteClass
definition: An assay that identifies an MHC ligand using a T cell response assay as a readout
definition source: IEDB
term editor: PERSON: Randi Vita, Bjoern Peters
IEDB alternative term: T cell recognition
example of usage: Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell.
editor preferred term: obsolete T cell recognition of eluted MHC ligand assay
deprecated: true
has curation status: IAO_0000120
has obsolescence reason: IAO_0000227
term replaced by: monospecific T cell recognition assay measuring MHC ligand processing and presentation

purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001994
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  intersection 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000281
subclass of: fluorescence detection binding assay
subclass of: OBI_0001994
definition: A purified MHC ligand binding on rate (kon) determination assay that uses fluorescence detection to measure direct ligand binding.
definition source: IEDB
term editor: IEDB
IEDB alternative term: on rate|purified MHC/direct/fluorescence|nM^-1s^-1
editor preferred term: purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-13 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: detection of specific nucleic acid polymers with complementary probes
subclass of: biological activity assay measuring epitope specific interleukin-13 production by T cells
definition: An assay of epitope specific interleukin-13 production by T cells that uses a detection of specific nucleic acids with complementary probes assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-13 release|RNA/DNA detection
editor preferred term: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells
has curation status: IAO_0000120

purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: OBI_0001988
subclass of: Restriction
  on property: has part
  some values from: fluorescence detection assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Restriction
    on property: has measurement unit label
    has value: UO_0000065
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
definition: A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses fluorescence detection to measure direct ligand binding and provides EC50 values determined under assay conditions where the EC50 approximates a KD value.
definition source: IEDB
term editor: IEDB
IEDB alternative term: dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM
editor preferred term: purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection
has curation status: IAO_0000120

cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001988
  intersection of: Restriction
    on property: has part
    some values from: 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: 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: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: radioactivity detection binding assay
subclass of: OBI_0001988
definition: A cell lysate MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
IEDB alternative term: dissociation constant KD|lysate MHC/competitive/radioactivity|nM
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
definition: An assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells that uses an intracellular cytokine staining assay.
IEDB alternative term: CCL3/MIP-1a release|ICS
term editor: IEDB
definition source: IEDB
editor preferred term: intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
has curation status: IAO_0000120

comparative phenotypic assessment
type: Class
subclass of: drawing a conclusion based on data
subclass of: OBI_0001834
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: Class
        union of: OBI_0100026
        union of: Restriction
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: conclusion textual entity
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: Class
        intersection of: Restriction
curator note: 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2
definition: Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference
term editor: Philly workshop 2011
definition source: Philly workshop 2011
editor preferred term: comparative phenotypic assessment
has curation status: IAO_0000123

material analysis service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: assay
subclass of: material service
definition: A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Matthew Brush
term editor: PERSON: Matthew Brush
example of usage: Services performing DNA sequencing or Cell Analysis
editor preferred term: material analysis service
has curation status: IAO_0000125

equilibrium association constant (KA)
type: Class
subclass of: binding constant
definition: A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
definition source: IEDB
example of usage: KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
term editor: PERSON: Bjoern Peters, Randi Vita
editor preferred term: equilibrium association constant (KA)
has curation status: IAO_0000120

cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001988
  intersection of: Restriction
    on property: has part
    some values from: 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: radioactivity detection binding assay
subclass of: OBI_0001988
definition: A cell bound MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
IEDB alternative term: dissociation constant KD|cellular MHC/competitive/radioactivity|nM
has curation status: IAO_0000120

cell bound MHC binding assay measuring binding of a MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: OBI_0002072
  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: OBI_0002072
definition: A MHC binding qualitative binding to ligand assay measuring MHC ligand binding using MHC present on cells.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC binding assay measuring binding of a MHC:ligand complex
IEDB alternative term: qualitative binding|cellular MHC
has curation status: IAO_0000120

access service
type: Class
subclass of: service
definition: A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service.
example of usage: A service that provides acess to a mass spectrometer.
editor note: Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process.
definition source: PERSON: Matthew Brush
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
editor preferred term: access service
has curation status: IAO_0000125

intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
subclass of: biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
definition: A T cell epitope specific tumor necrosis factor (ligand) superfamily member 11 production assay that uses an intracellular cytokine staining assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: TNFSF11/RANKL release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
has curation status: IAO_0000120

assay measuring a binding constant of a MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: OBI_1110126
  intersection of: Restriction
    on property: has_specified_output
    some values from: binding constant
subclass of: binding constant determination assay
subclass of: OBI_1110126
definition: A MHC:ligand binding assay that measures a binding constant.
definition source: IEDB
term editor: IEDB
editor preferred term: assay measuring a binding constant of a MHC:ligand complex
IEDB alternative term: binding constant|binding assay
has curation status: IAO_0000120

rate measurement datum
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that represents the number of events occuring over a time interval
definition source: IEDB
term editor: PERSON: Bjoern Peters, Randi Vita
example of usage: The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
editor preferred term: rate measurement datum
has curation status: IAO_0000120

purified MHC binding assay measuring binding of a MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: OBI_0002072
  intersection 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: OBI_0002072
definition: A MHC binding qualitative binding to ligand assay using MHC in a purified MHC molecule preparation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: purified MHC binding assay measuring binding of a MHC:ligand complex
IEDB alternative term: qualitative binding|purified MHC
has curation status: IAO_0000120

cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection
type: Class
subclass of: radioactivity detection binding assay
subclass of: cell lysate MHC binding assay measuring binding of a MHC:ligand complex
subclass of: Restriction
  on property: has part
  some values from: radioactivity detection
subclass 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
definition: A cell lysate MHC binding assay that uses radioactivity detection to detect direct binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection
IEDB alternative term: qualitative binding|lysate MHC/direct/radioactivity
has curation status: IAO_0000120

material storage service
type: Class
equivalent class: Class
  intersection of: material service
  intersection of: Restriction
    on property: provides_service_consumer_with
    some values from: OBI_0302893
subclass of: material maintenance service
example of usage: A service that offers liquid nitrogen stroage.
definition: A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
term editor: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
definition source: PERSON: Matthew Brush
editor preferred term: material storage service
has curation status: IAO_0000125

cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001990
  intersection of: Restriction
    on property: has part
    some values from: radioactivity detection
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000031
subclass of: radioactivity detection binding assay
subclass of: OBI_0001990
definition: A cell bound MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding.
term editor: IEDB
definition source: IEDB
editor preferred term: cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
IEDB alternative term: half life|cellular MHC/direct/radioactivity|min
has curation status: IAO_0000120

cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001990
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000031
subclass of: fluorescence detection binding assay
subclass of: OBI_0001990
definition: A cell bound MHC ligand half life of binding determination assay that uses fluorescence detection to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
IEDB alternative term: half life|cellular MHC/direct/fluorescence|min
has curation status: IAO_0000120

obsolete cell lysate MHC binding constant determination assay
type: Class
subclass of: ObsoleteClass
definition: An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant.
definition source: IEDB
term editor: PERSON: Bjoern Peters
editor preferred term: obsolete cell lysate MHC binding constant determination assay
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001991
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: fluorescence detection binding assay
subclass of: OBI_0001991
definition: A cell bound MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding.
definition source: IEDB
term editor: IEDB
editor preferred term: cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
IEDB alternative term: half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0001772
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: OBI_0001772
subclass of: OBI_1110178
definition: A T cell epitope specific interleukin-17F production assay that uses an intracellular cytokine staining assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-17F release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells
has curation status: IAO_0000120

material processing service
type: Class
subclass of: material service
subclass of: Restriction
  on property: provides_service_consumer_with
  some values from: material processing
example of usage: A service for cell line creation. A service providing cel line immortalization.
definition: A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
editor preferred term: material processing service
has curation status: IAO_0000125

purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection
type: Class
subclass of: OBI_0001989
subclass of: Restriction
  on property: has_specified_output
  some values from: Restriction
    on property: has measurement unit label
    has value: UO_0000065
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 part
  some values from: radioactivity detection
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
definition: A purified MHC ligand binding equilibrium dissociation constant (KD) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value.
term editor: IEDB
definition source: IEDB
IEDB alternative term: dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM
editor preferred term: purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection
has curation status: IAO_0000120

cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001990
  intersection of: Restriction
    on property: has part
    some values from: 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: Restriction
      on property: has measurement unit label
      has value: UO_0000031
subclass of: radioactivity detection binding assay
subclass of: OBI_0001990
definition: A cell lysate MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
IEDB alternative term: half life|lysate MHC/direct/radioactivity|min
has curation status: IAO_0000120

50% dissociation of binding temperature (Tm)
type: Class
subclass of: binding datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: UO_0000005
editor preferred term: 50% dissociation of binding temperature (Tm)
definition: A binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound.
definition source: IEDB
term editor: PERSON: Bjoern Peters, Randi Vita
example of usage: Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated.
alternative term: melting temperature (Tm)
has curation status: IAO_0000120

cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001993
  intersection of: Restriction
    on property: has part
    some values from: 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: Restriction
      on property: has measurement unit label
      has value: UO_0000106
subclass of: radioactivity detection binding assay
subclass of: OBI_0001993
definition: A cell lysate MHC ligand binding off rate measurement (koff) determination assay that uses radioactivity detection to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection
IEDB alternative term: off rate|lysate MHC/direct/radioactivity|1/s
has curation status: IAO_0000120

purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001992
  intersection of: Restriction
    on property: has part
    some values from: 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: purified MHC molecule preparation
      intersection of: Restriction
        on property: has part
        some values from: MHC protein complex
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: radioactivity detection binding assay
subclass of: OBI_0001992
definition: A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM
editor preferred term: purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
has curation status: IAO_0000120

purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001993
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  intersection 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000106
subclass of: fluorescence detection binding assay
subclass of: OBI_0001993
definition: A purified MHC ligand binding off rate measurement (koff) determination assay that uses fluorescence detection to measure direct ligand binding.
term editor: IEDB
definition source: IEDB
IEDB alternative term: off rate|purified MHC/direct/fluorescence|1/s
editor preferred term: purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: vascular endothelial growth factor production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells.
definition source: IEDB
term editor: IEDB
IEDB alternative term: VEGF release|biological activity
editor preferred term: biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells
has curation status: IAO_0000120

equilibrium dissociation constant (KD) approximated by IC50
type: Class
subclass of: binding constant
subclass of: half maximal inhibitory concentration (IC50)
definition: A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
term editor: PERSON: Bjoern Peters, Randi Vita
editor preferred term: equilibrium dissociation constant (KD) approximated by IC50
definition source: http://dx.doi.org/10.1016/0006-2952(73)90196-2
has curation status: IAO_0000120

obsolete cell bound MHC binding constant determination assay
type: Class
subclass of: ObsoleteClass
definition: An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant.
definition source: IEDB
term editor: PERSON: Bjoern Peters
editor preferred term: obsolete cell bound MHC binding constant determination assay
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
curator note: 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
definition: A sequence data item that is about the primary structure of DNA
editor preferred term: DNA sequence data
term editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: IAO_0000120

obsolete cell lysate MHC competitive binding assay using radioactivity detection
type: Class
subclass of: ObsoleteClass
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: cell lysate MHC competitive binding using radioactivity
definition: competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate
editor preferred term: obsolete cell lysate MHC competitive binding assay using radioactivity detection
deprecated: true
has curation status: IAO_0000122
has obsolescence reason: IAO_0000227
term replaced by: cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection

assigning gene property based on phenotypic assessment
type: Class
subclass of: drawing a conclusion based on data
subclass of: Restriction
  on property: has_specified_input
  some values from: Restriction
    on property: is_specified_output_of
    some values from: comparative phenotypic assessment
definition: Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result.
term editor: Philly workshop 2011
definition source: Philly workshop 2011
editor preferred term: assigning gene property based on phenotypic assessment
has curation status: IAO_0000123

obsolete purified MHC binding constant determination assay
type: Class
subclass of: ObsoleteClass
definition: An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant.
definition source: IEDB
term editor: PERSON: Bjoern Peters
editor preferred term: obsolete purified MHC binding constant determination assay
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-22 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-22 production by T cells
definition: An assay of epitope specific interleukin-22 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-22 release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells
has curation status: IAO_0000120

ELISA measuring epitope specific vascular endothelial growth factor production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells
  intersection of: Restriction
    on property: has part
    some values from: enzyme-linked immunosorbent assay
subclass of: biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells
definition: An assay of epitope specific vascular endothelial growth factor production by T cells that uses an ELISA.
editor preferred term: ELISA measuring epitope specific vascular endothelial growth factor production by T cells
term editor: IEDB
definition source: IEDB
IEDB alternative term: VEGF release|ELISA
has curation status: IAO_0000120

cell lysate MHC binding assay measuring binding of a MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: OBI_0002072
  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
subclass of: OBI_0002072
definition: A MHC binding qualitative binding to ligand assay using MHC in a cell lysate.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell lysate MHC binding assay measuring binding of a MHC:ligand complex
IEDB alternative term: qualitative binding|lysate MHC
has curation status: IAO_0000120

material transport service
type: Class
subclass of: material service
example of usage: A service for chemical disposal
definition: A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Carlo Torniai
term editor: PERSON: Matthew Brush
editor preferred term: material transport service
has curation status: IAO_0000125

equilibrium dissociation constant (KD) approximated by EC50
type: Class
subclass of: binding constant
subclass of: half maximal effective concentration (EC50)
definition: A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
definition source: Assay Development: Fundamentals and Practices, By Ge Wu, page 74
term editor: PERSON: Bjoern Peters, Randi Vita
editor preferred term: equilibrium dissociation constant (KD) approximated by EC50
has curation status: IAO_0000120

obsolete cell bound MHC direct binding assay
type: Class
subclass of: ObsoleteClass
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: cell bound MHC direct binding
definition: direct binding assay measuring MHC ligand binding using MHC derived from a cell
editor preferred term: obsolete cell bound MHC direct binding assay
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000122

half life of binding datum
type: Class
subclass of: binding constant
subclass of: half life datum (t 1/2)
definition: A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
definition source: IEDB
term editor: PERSON: Bjoern Peters, Randi Vita
example of usage: The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
editor preferred term: half life of binding datum
has curation status: IAO_0000120

purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display
type: Class
subclass of: purified MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: phage display binding assay
definition: A purified MHC binding assay that uses a phage display binding assay to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display
IEDB alternative term: qualitative binding|purified MHC/direct/phage display
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific interleukin-7 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-7 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-7 production by T cells
definition: An assay of epitope specific interleukin-7 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-7 release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific interleukin-7 production by T cells
has curation status: IAO_0000120

purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
type: Class
equivalent class: Class
  intersection of: OBI_0001990
  intersection of: Restriction
    on property: has part
    some values from: radioactivity detection
  intersection 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000031
subclass of: radioactivity detection binding assay
subclass of: OBI_0001990
definition: A purified MHC ligand half life of binding determination assay that uses radioactivity detection to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: half life|purified MHC/direct/radioactivity|min
editor preferred term: purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
has curation status: IAO_0000120

biological activity assay measuring epitope specific interleukin-7 production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: interleukin-7 production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-7 release|biological activity
editor preferred term: biological activity assay measuring epitope specific interleukin-7 production by T cells
has curation status: IAO_0000120

binding
type: Class
subclass of: biological_process
editor note: 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
example of usage: A peptide binding to an MHC molecule to form a complex.
definition source: IEDB
term editor: PERSON: Bjoern Peters, Randi Vita
definition: The process of material entities forming complexes.
editor preferred term: binding
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_0001773
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: OBI_0001773
subclass of: OBI_1110178
definition: A T cell epitope specific interleukin-17A production assay that uses an intracellular cytokine staining assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-17A release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells
has curation status: IAO_0000120

purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: purified MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: fluorescence detection assay
definition: A purified MHC binding assay that uses fluorescence detection to measure direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection
IEDB alternative term: qualitative binding|purified MHC/direct/fluorescence
has curation status: IAO_0000120

direct binding assay
type: Class
subclass of: binding assay
example of usage: Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody.
definition source: IEDB
term editor: PERSON:Bjoern Peters, Randi Vita
definition: a binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand.
editor preferred term: direct binding assay
has curation status: IAO_0000120

purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001991
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  intersection 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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: fluorescence detection binding assay
subclass of: OBI_0001991
definition: A purified MHC ligand binding half maximal effective concentration (EC50) determination assay that uses fluorescence detection to measure direct ligand binding.
definition source: IEDB
term editor: IEDB
IEDB alternative term: half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM
editor preferred term: purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

competitive inhibition of binding assay
type: Class
subclass of: binding assay
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
definition: A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material.
example of usage: Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide.
term editor: IEDB
definition source: IEDB
editor preferred term: competitive inhibition of binding assay
has curation status: IAO_0000120

cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: cell bound MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: fluorescence detection assay
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
definition: A cell bound MHC binding assay that uses fluorescence to detect loss of binding of a known reference ligand due to competition by the ligand under investigation
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection
IEDB alternative term: qualitative binding|cellular MHC/competitive/fluorescence
has curation status: IAO_0000120

X-ray crystallography assay determining the 3D structure of a MHC:ligand complex
type: Class
equivalent class: Class
  intersection of: OBI_0002050
  intersection of: Restriction
    on property: has part
    some values from: X-ray crystallography assay
  intersection 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
  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: has measurement unit label
      has value: UO_0000019
subclass of: OBI_0002050
IEDB alternative term: 3D structure|x-ray crystallography|angstroms
definition: A MHC binding 3D structure determination of MHC molecule:epitope complex assay that uses an X-ray crystallography assay.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: X-ray crystallography assay determining the 3D structure of a MHC:ligand complex
has curation status: IAO_0000120

PDB file chain
type: Class
subclass of: 3D structural organization datum
subclass of: Restriction
  on property: part of
  some values from: PDB file
definition: A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities
definition source: IEDB
editor preferred term: PDB file chain
term editor: PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum
example of usage: The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
has curation status: IAO_0000120

cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition
type: Class
equivalent class: Class
  intersection of: OBI_0001992
  intersection of: Restriction
    on property: has part
    some values from: OBI_1110037
  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
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: OBI_0001992
definition: A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding.
term editor: IEDB
definition source: IEDB
editor preferred term: cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition
IEDB alternative term: half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM
has curation status: IAO_0000120

data maintenance service
type: Class
subclass of: data service
example of usage: A database management service, a web hosting service.
definition: A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance.
term editor: PERSON: Carlo Torniai
definition source: PERSON: Matthew Brush
term editor: PERSON: Matthew Brush
editor preferred term: data maintenance service
has curation status: IAO_0000125

cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
type: Class
subclass of: radioactivity detection binding assay
subclass of: cell bound MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: radioactivity detection
definition: A cell bound MHC binding assay that uses radioactivity detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: IEDB
editor preferred term: cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
IEDB alternative term: qualitative binding|cellular MHC/competitive/radioactivity
has curation status: IAO_0000120

biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
type: Class
equivalent class: Class
  intersection of: OBI_1110129
  intersection 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: granulocyte colony-stimulating factor production
subclass of: OBI_1110129
definition: A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells.
IEDB alternative term: G-CSF release|biological activity
term editor: IEDB
definition source: IEDB
editor preferred term: biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-21 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-21 production by T cells
definition: An assay of epitope specific interleukin-21 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-21 release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells
has curation status: IAO_0000120

cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection
type: Class
subclass of: radioactivity detection binding assay
subclass of: cell bound MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: radioactivity detection
definition: A cell bound MHC binding assay that uses radioactivity detection to detect direct binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection
IEDB alternative term: qualitative binding|cellular MHC/direct/radioactivity
has curation status: IAO_0000120

binding off rate measurement datum (koff)
type: Class
subclass of: binding constant
subclass of: rate measurement datum
definition: A rate measurement datum of how quickly bound complexes disassociate
definition source: IEDB
term editor: PERSON: Bjoern Peters, Randi Vita
editor preferred term: binding off rate measurement datum (koff)
has curation status: IAO_0000120

purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: purified MHC binding assay measuring binding of a MHC:ligand complex
subclass of: Restriction
  on property: has_specified_output
  some values from: Restriction
    on property: has measurement unit label
    has value: UO_0000027
subclass of: Restriction
  on property: has part
  some values from: fluorescence detection assay
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: 50% dissociation of binding temperature (Tm)
IEDB alternative term: 50% dissociation temperature|purified MHC/direct/fluorescence|�C
definition: A purified MHC binding assay that uses fluorescence detection to measure the 50% dissociation of binding temperature of direct ligand binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

binding on rate measurement datum (kon)
type: Class
subclass of: binding constant
subclass of: rate measurement datum
definition: A rate measurement datum of how quickly bound complexes form
definition source: IEDB
term editor: PERSON: Bjoern Peters, Randi Vita
editor preferred term: binding on rate measurement datum (kon)
has curation status: IAO_0000120

cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection
type: Class
subclass of: fluorescence detection binding assay
subclass of: cell bound MHC binding assay measuring binding of a MHC:ligand complex
subclass of: Restriction
  on property: has part
  some values from: fluorescence detection assay
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
definition: A cell bound MHC binding assay that uses fluorescence detection to detect direct binding.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection
IEDB alternative term: qualitative binding|cellular MHC/direct/fluorescence
has curation status: IAO_0000120

biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
  intersection 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: tumor necrosis factor (ligand) superfamily member 11 production
subclass of: biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
definition: An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production.
term editor: IEDB
definition source: IEDB
IEDB alternative term: TNFSF11/RANKL release|biological activity
editor preferred term: biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
has curation status: IAO_0000120

purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection
type: Class
subclass of: radioactivity detection binding assay
subclass of: purified MHC binding assay measuring binding of a MHC:ligand complex
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 part
  some values from: radioactivity detection
definition: A purified MHC binding assay that uses radioactivity detection to measure direct ligand binding.
definition source: IEDB
term editor: IEDB
editor preferred term: purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection
IEDB alternative term: qualitative binding|purified MHC/direct/radioactivity
has curation status: IAO_0000120

intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-8 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: flow cytometry assay
subclass of: biological activity assay measuring epitope specific interleukin-8 production by T cells
definition: An assay of epitope specific interleukin-8 production by T cells that uses an intracellular cytokine staining assay.
term editor: IEDB
definition source: IEDB
IEDB alternative term: IL-8 release|ICS
editor preferred term: intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells
has curation status: IAO_0000120

cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells
type: Class
equivalent class: Class
  intersection of: biological activity assay measuring epitope specific interleukin-23 production by T cells
  intersection of: Restriction
    on property: has part
    some values from: cytometric bead array assay
subclass of: biological activity assay measuring epitope specific interleukin-23 production by T cells
definition: An assay of epitope specific interleukin-23 production by T cells that uses a cytometric bead array assay.
definition source: IEDB
term editor: IEDB
IEDB alternative term: IL-23 release|cytometric bead array
editor preferred term: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells
has curation status: IAO_0000120

obsolete purified MHC direct binding assay
type: Class
subclass of: ObsoleteClass
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition: direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation
editor preferred term: obsolete purified MHC direct binding assay
IEDB alternative term: purified MHC direct binding
deprecated: true
has obsolescence reason: IAO_0000103
has curation status: IAO_0000122

epitope specific vascular endothelial growth factor production by T cells
type: Class
equivalent class: Class
  intersection of: vascular endothelial growth factor production
  intersection of: Restriction
    on property: process is result of
    some values from: OBI_1110057
subclass of: vascular endothelial growth factor production
subclass of: epitope specific cytokine production by T cells
definition: A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope.
curator note: Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl
definition source: IEDB (QTT)
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
editor preferred term: epitope specific vascular endothelial growth factor production by T cells
has curation status: IAO_0000122

purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
type: Class
equivalent class: Class
  intersection of: OBI_0001992
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
  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: purified MHC molecule preparation
      intersection of: Restriction
        on property: has part
        some values from: MHC protein complex
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: has measurement unit label
      has value: UO_0000065
subclass of: fluorescence detection binding assay
subclass of: OBI_0001992
definition: A purified MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses fluorescence detection to detect loss of binding of a known reference ligand due to competition by the ligand under investigation.
definition source: IEDB
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB alternative term: half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM
editor preferred term: purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
has curation status: IAO_0000120

GenBank ID
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: sequence data
editor preferred term: GenBank ID
NIAID GSCID-BRC alternative term: GenBank Record ID
Source: NIAID GSCID-BRC
definition: A CRID symbol uniquely indentifies the submitted GeneBank sequence record.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
has curation status: IAO_0000120

investigation description
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: investigation
ISA alternative term: study description
definition: A textual entity that describes an investigation.
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: investigation description
NIAID GSCID-BRC alternative term: project description
has curation status: IAO_0000120

specimen identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: OBI_0100051
Source: NIAID GSCID-BRC
definition: A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
NIAID GSCID-BRC alternative term: Specimen ID
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
alternative term: specimen ID
editor preferred term: specimen identifier
has curation status: IAO_0000120

PubMed ID
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  on class: publication
  qualified cardinality: 1
NIAID GSCID-BRC alternative term: Publication Citation
definition: A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
editor note: Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/
Source: NIAID GSCID-BRC
alternative term: PMID
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: PubMed ID
alternative term: PubMed Identifier
definition source: Website: http://en.wikipedia.org/wiki/Wikipedia:PMID
has curation status: IAO_0000120

average depth of sequence coverage
type: Class
subclass of: average value
Source: NIAID GSCID-BRC
definition: An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
NIAID GSCID-BRC alternative term: Depth of Coverage - Average
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: average depth of sequence coverage
has curation status: IAO_0000120

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: specimen collection process
NIAID GSCID-BRC alternative term: Specimen Collection Date
definition: A time measurement datum that is the measure of the time when the specimens are collected.
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
alternative term: collection date
editor preferred term: specimen collection time measurement datum
has curation status: IAO_0000120

latitude coordinate measurement datum
type: Class
subclass of: measurement datum
Source: NIAID GSCID-BRC
NIAID GSCID-BRC alternative term: Specimen Collection Location - Latitude
definition: A measurement datum that is the measure of the latitude coordinate of a site.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
alternative term: latitude
editor preferred term: latitude coordinate measurement datum
has curation status: IAO_0000120

longitude coordinate measurement datum
type: Class
subclass of: measurement datum
NIAID GSCID-BRC alternative term: Specimen Collection Location - Longitude
definition: A measurement datum that is the measure of the longitude coordinate of a site.
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
alternative term: longitude
editor preferred term: longitude coordinate measurement datum
has curation status: IAO_0000120

investigation title
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: denotes
  some values from: investigation
ISA alternative term: study title
definition: A textual entity that denotes an investigation.
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person:Chris Stoeckert, Jie Zheng
editor preferred term: investigation title
NIAID GSCID-BRC alternative term: project title
has curation status: IAO_0000120

organism identification objective
type: Class
subclass of: biological feature identification objective
definition: A biological feature identification objective to identify the organism species in a specimen.
definition source: Penn Group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: organism identification objective
has curation status: IAO_0000120

organism identification assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: organism identification objective
subclass of: assay
subclass of: Class
  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: OBI_0100026
  intersection 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: OBI_0100026
definition: An assay that identifies the organism species in a specimen.
NIAID GSCID-BRC alternative term: Organism Detection Method
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: organism identification assay
has curation status: IAO_0000120

sequence annotation algorithm
type: Class
subclass of: algorithm
Source: NIAID GSCID-BRC
NIAID GSCID-BRC alternative term: Annotation Algorithm
definition: An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
editor preferred term: sequence annotation algorithm
has curation status: IAO_0000120

Bioinformatics Resource Center
type: Class
subclass of: organization
definition: An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
alternative term: BRC
editor preferred term: Bioinformatics Resource Center
Source: NIAID GSCID-BRC
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
has curation status: IAO_0000120

country name
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: denotes
  some values from: geographic location
Source: NIAID GSCID-BRC
NIAID GSCID-BRC alternative term: Specimen Collection Location - Country
definition: A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Website: http://en.wikipedia.org/wiki/Country
editor preferred term: country name
has curation status: IAO_0000120

investigation identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: investigation
definition: A CRID symbol used to identify an investigation.
Source: NIAID GSCID-BRC
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zhneg
editor preferred term: investigation identifier
NIAID GSCID-BRC alternative term: project ID
has curation status: IAO_0000120

grant identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: OBI_0001636
Source: NIAID GSCID-BRC
definition: A CRID symbol used to identify a grant.
definition source: NIAID GSCID-BRC metadata working group
term editor: Person: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC alternative term: grant ID
editor preferred term: grant identifier
has curation status: IAO_0000120

analytical chromatography
type: Class
equivalent class: Class
  intersection of: analyte 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: chromatography column
  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: chromatography consumable
subclass of: analyte assay
definition: An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material.
example of usage: Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column.
term editor: IEDB
definition source: IEDB
editor preferred term: analytical chromatography
has curation status: IAO_0000120

electron microscopy imaging assay
type: Class
equivalent class: Class
  intersection of: imaging 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: electron microscope
subclass of: OBI_0002119
definition: An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material.
term editor: IEDB
definition source: IEDB
example of usage: Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure.
editor preferred term: electron microscopy imaging assay
has curation status: IAO_0000120

immuno staining assay
type: Class
subclass of: OBI_0600017
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: REO_0000171
      intersection of: Restriction
        on property: inheres in
        some values from: immunoglobulin complex, circulating
  intersection of: Restriction
    on property: has_specified_input
    some values from: immunoglobulin complex, circulating
definition: A detection of molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity.
example of usage: Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye.
definition source: IEDB
term editor: IEDB
editor preferred term: immuno staining assay
has curation status: IAO_0000120

purified material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: purification
subclass of: processed material
definition: A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component
example of usage: A mixture of peptide molecules that has been run through an HPLC column to remove 65
term editor: GROUP: OBI call
definition source: OBI conference call
editor preferred term: purified material
has curation status: IAO_0000120

calorimetric binding assay
type: Class
equivalent class: Class
  intersection of: binding assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
subclass of: binding assay
definition: A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy.
example of usage: A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (ΔH) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell .
definition source: IEDB
term editor: IEDB
editor preferred term: calorimetric binding assay
has curation status: IAO_0000120