OLAM: Ontology of Laboratory Animal Medicine
type: Ontology
Contributor: Bob Dysko
creator: Yongqun "Oliver" He (YH)
date: 2-19-2021
description: OLAM is a biomedical ontology in the area of laboratory animal medicine.
Format: OWL-DL
subject: Laboratory animal medicine
version info: Vision Release: 1.0.12

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

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

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

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

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

textual definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
textual definition: English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
textual definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
textual definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has exact synonym: DEFINITION
label: definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
textual 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 editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
database_cross_reference: IAO:0000116
has_obo_namespace: uberon
id: editor_note
is metadata tag: 1
shorthand: editor_note

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

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

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

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
textual 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.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: ready for release
textual definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
database_cross_reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: 1
shorthand: curator_notes
label: curator notes

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

expand expression to
type: AnnotationProperty

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

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

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

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

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

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

temporal interpretation
type: AnnotationProperty
textual definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

logical macro assertion
type: AnnotationProperty
textual definition: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

logical macro assertion on a property
type: AnnotationProperty
textual definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
sub property of: logical macro assertion on a property

has_rank
type: AnnotationProperty
textual definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy
comment: This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored

Contributor
type: AnnotationProperty
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
has_obo_namespace: uberon
id: dc-contributor
is metadata tag: 1
shorthand: dc-contributor
comment: An entity responsible for making contributions to the content of the resource.
label: contributor

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

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

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

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

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

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

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

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has exact synonym
type: AnnotationProperty
textual definition: Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has exact synonym: FULL_SYN
has exact synonym: Synonym with Source Data
label: has_exact_synonym

has_obo_namespace
type: AnnotationProperty
comment: disease_ontology

has_related_synonym
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

label
type: AnnotationProperty
editor preferred label: label

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
textual definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See 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'.
alternative term: part_of
imported from: go.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: ro.owl
imported from: uberon.owl
temporal interpretation: axiom holds for all times
database_cross_reference: BFO:0000050
has_obo_namespace: uberon
id: part_of
shorthand: part_of

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
sub property of: overlaps
sub property of: has material contribution from
type: TransitiveProperty
editor preferred label: 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)
textual definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See 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'.
alternative term: has_part
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: ro.owl
imported from: uberon.owl
temporal interpretation: axiom holds for all times
database_cross_reference: BFO:0000051
has_obo_namespace: uberon
id: has_part
shorthand: has_part

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

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

preceded_by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
editor preferred label: preceded by
textual definition: X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
textual definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
imported from: uberon.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
database_cross_reference: BFO:0000062
has exact synonym: is preceded by
has exact synonym: takes place after
has_obo_namespace: uberon
id: preceded_by
in_subset: ro-eco
shorthand: preceded_by
label: preceded by

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: happens during
editor preferred label: precedes
textual definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
imported from: uberon.owl
database_cross_reference: BFO:0000063
has_obo_namespace: uberon
id: precedes
in_subset: ro-eco
shorthand: precedes

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

contains process
type: ObjectProperty
equivalent property:
  inverse of: occurs in
editor preferred label: site of
textual 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
imported from: obi.owl
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
textual definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
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 editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: iao.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

denotes
type: ObjectProperty
sub property of: is about
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.
textual 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
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
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
imported from: obi.owl

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
editor preferred label: is_supported_by_data
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has curation status: ready for release
textual 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
definition editor: OBI
definition source: OBI
definition source: Philly 2011 workshop
imported from: obi.owl

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
textual 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.
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: planned process
editor preferred label: 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: ready for release
textual 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

obsolete_has_quality
type: ObjectProperty
sub property of: ObsoleteProperty
editor preferred label: has_quality
has curation status: ready for release
textual definition: A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
editor note: replaced by: http://purl.obolibrary.org/obo/BFO_0000086
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungall
has obsolescence reason: term imported
imported from: obi.owl
deprecated: true

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
has curation status: ready for release
textual 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

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

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

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

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: ready for release
textual 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

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

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

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: ready for release
textual 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.
definition editor: OBI
definition source: OBI
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: has value specification
has curation status: metadata complete
textual definition: A relation between an information content entity and a value specification that specifies its value.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

is animal model for disease
type: ObjectProperty
textual definition: An object property that represents a relation beween an animal organism and a disease

absent in process
type: ObjectProperty

absent in location
type: ObjectProperty

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
textual 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 note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
imported from: obi.owl
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
textual 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 note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
imported from: obi.owl
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
equivalent property:
  inverse of: has participant
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: 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
textual definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: obi.owl

has participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
domain: occurrent
range: continuant
editor preferred label: 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)
textual definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
imported from: obi.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
textual 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.
imported from: obi.owl

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
textual 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.
imported from: obi.owl

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
textual definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
imported from: obi.owl

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
textual definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
imported from: obi.owl

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

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

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

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

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded_by
definition editor: David Osumi-Sutherland
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
definition editor: David Osumi-Sutherland
alternative term: io
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
in_subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: d
alternative term: during
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
in_subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
definition editor: David Osumi-Sutherland
alternative term: o
alternative term: overlaps
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
in_subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part
has curation status: pending final vetting
textual definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
imported from: uberon.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: ro-eco

develops_from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: has material contribution from
inverse of: develops_into
type: TransitiveProperty
property chain axiom: part of
imported from: OAE: Ontology of Adverse Events
imported from: uberon.owl
database_cross_reference: RO:0002202
has_obo_namespace: uberon
id: develops_from
shorthand: develops_from

develops_into
type: ObjectProperty
sub property of: has potential to develop into
imported from: OAE: Ontology of Adverse Events
imported from: uberon.owl
database_cross_reference: RO:0002203
has_obo_namespace: uberon
id: develops_into
shorthand: develops_into

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
definition editor: Chris Mungall
definition source: Allen's interval algebra
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
Source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has developmental contribution from
type: ObjectProperty
sub property of: has material contribution from
type: TransitiveProperty
property chain axiom: has part
property chain axiom: develops_from
imported from: OAE: Ontology of Adverse Events
imported from: uberon.owl
database_cross_reference: RO:0002254
has_obo_namespace: uberon
id: has_developmental_contribution_from
shorthand: has_developmental_contribution_from

mereotopologically related to
type: ObjectProperty
textual definition: A mereological relationship or a topological relationship
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
imported from: OAE: Ontology of Adverse Events
imported from: ro.owl
temporal interpretation: axiom holds for all times

has potential to develop into
type: ObjectProperty
textual definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
imported from: OAE: Ontology of Adverse Events
imported from: uberon.owl
database_cross_reference: RO:0002387
has_obo_namespace: uberon
id: has_potential_to_develop_into
shorthand: has_potential_to_develop_into

has material contribution from
type: ObjectProperty
type: TransitiveProperty
property chain axiom: has part
property chain axiom: develops_from
imported from: OAE: Ontology of Adverse Events
imported from: uberon.owl
database_cross_reference: RO:0002507
has_obo_namespace: uberon
id: has_material_contribution_from
shorthand: has_material_contribution_from

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

continuant
type: Class
subclass of: entity
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
textual 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
imported from: bfo.owl
imported from: dron.owl
imported from: envo.owl
imported from: iao.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: ro.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

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

independent continuant
type: Class
subclass of: continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
textual 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.
textual 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])
imported from: obi.owl
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

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

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

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

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
textual 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.
imported from: obi.owl
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

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

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
textual 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.
textual 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])
textual definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: obi.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

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

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

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

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
textual 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.
textual 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])
imported from: dron.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

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

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

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

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

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
textual 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])
imported from: obi.owl
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]

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

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
imported from: obi.owl
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])

primary bacterial infectious disease
type: Class
subclass of: disease
textual definition: A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0050338
in_subset: DO FlyBase slim

brucellosis
type: Class
subclass of: primary bacterial infectious disease
textual definition: A primary bacterial infectious disease that is caused by the bacteria of the genus Brucella, when humans come in contact with contaminated animals or animal products or ingestion of infected food products. The disease has_symptom fever, has_symptom sweat, has_symptom headache, has_symptom back pain, has_symptom physical weakness, has_symptom joint pain and has_symptom fatigue.
imported from: doid.owl
has_alternative_id: DOID:0050060
database_cross_reference: GARD:5966
database_cross_reference: ICD10CM:A23
database_cross_reference: ICD10CM:A23.9
database_cross_reference: ICD9CM:023
database_cross_reference: ICD9CM:023.9
database_cross_reference: MESH:D002006
database_cross_reference: NCI:C84602
database_cross_reference: SNOMEDCT_US_2018_03_01:75702008
database_cross_reference: UMLS_CUI:C0006309
has exact synonym: Maltese fever
has exact synonym: undulant fever
has_obo_namespace: disease_ontology
has_related_synonym: Bang's disease
has_related_synonym: Gibraltar fever
has_related_synonym: Malta fever
has_related_synonym: Mediterranean fever
id: DOID:11077
in_subset: NCIthesaurus
in_subset: gram-negative bacterial infectious disease
in_subset: zoonotic infectious disease

Brucella melitensis brucellosis
type: Class
subclass of: brucellosis
textual definition: A brucellosis that involves an infection caused by Brucella melitensis [NCBITaxon:29459] in cattle, goats, sheep and humans. The disease has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom limb pain and has_symptom back pain.
imported from: doid.owl
database_cross_reference: ICD10CM:A23.0
database_cross_reference: ICD9CM:023.0
database_cross_reference: SNOMEDCT_US_2018_03_01:30789005
database_cross_reference: UMLS_CUI:C0302362
has_obo_namespace: disease_ontology
id: DOID:14456
in_subset: gram-negative bacterial infectious disease
in_subset: zoonotic infectious disease

Brucella abortus brucellosis
type: Class
subclass of: brucellosis
textual definition: A brucellosis that involves an infection caused by Brucella abortus [NCBITaxon:235] in cattle and humans. The disease has_symptom fever, has_symptom chills, has_symptom sweats, has_symptom weight loss, has_symptom malaise, has_symptom headaches, has_symptom myalgia, and has_symptom arthralgia.
imported from: doid.owl
database_cross_reference: ICD10CM:A23.1
database_cross_reference: ICD9CM:023.1
database_cross_reference: MESH:D002007
database_cross_reference: SNOMEDCT_US_2018_03_01:9060000
database_cross_reference: UMLS_CUI:C0302363
has_obo_namespace: disease_ontology
id: DOID:14457
in_subset: gram-negative bacterial infectious disease
in_subset: zoonotic infectious disease

tuberculosis
type: Class
subclass of: primary bacterial infectious disease
textual definition: A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes.
imported from: doid.owl
has_alternative_id: DOID:10096
has_alternative_id: DOID:12688
has_alternative_id: DOID:12691
has_alternative_id: DOID:415
has_alternative_id: DOID:9901
has_alternative_id: DOID:9902
database_cross_reference: GARD:7827
database_cross_reference: MESH:D014375
database_cross_reference: SNOMEDCT_US_2018_03_01:15202009
database_cross_reference: UMLS_CUI:C0041295
has_obo_namespace: disease_ontology
id: DOID:399
in_subset: gram-positive bacterial infectious disease

disease
type: Class
subclass of: disposition
textual definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: doid.owl
database_cross_reference: MESH:D004194
database_cross_reference: NCI:C2991
database_cross_reference: SNOMEDCT_US_2018_03_01:64572001
database_cross_reference: UMLS_CUI:C0012634
has_obo_namespace: disease_ontology
id: DOID:4
in_subset: NCIthesaurus

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

immune response
type: Class
subclass of: biological_process
textual definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl
has_obo_namespace: biological_process
id: GO:0006955
comment: This term was improved by GO_REF:0000022. It was redefined and moved.

biological_process
type: Class
subclass of: process
editor preferred label: biological_process
textual definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl
imported from: obi.owl
created by: janelomax
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database_cross_reference: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
textual 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.
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?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: obi.owl

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
textual definition: a directive information entity that describes an action the bearer will take
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: obi.owl

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
textual 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.
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.
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: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: dron.owl
imported from: iao.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
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"
has curation status: pending final vetting
textual definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another 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://github.com/information-artifact-ontology/IAO/issues/154).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
textual definition: A generically dependent continuant that is about some thing.
textual definition: An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some 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).
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.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: dron.owl
imported from: iao.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: ready for release
textual definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: obi.owl

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: pending final vetting
textual definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: dron.owl
imported from: iao.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

data set
type: Class
subclass of: data item
editor preferred label: data set
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).
has curation status: pending final vetting
textual 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.
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 editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
imported from: obi.owl

data about an ontology part
type: Class
subclass of: data item
textual definition: data about an ontology part is a data item about a part of an ontology, for example a term
definition editor: Person:Alan Ruttenberg
imported from: dron.owl
imported from: iao.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

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
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
textual 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.
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.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: obi.owl
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

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred label: measurement datum
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,}.
has curation status: pending final vetting
textual 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.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: conclusion based on data
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: 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: metadata complete
textual definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
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 editor: Person:Alan Ruttenberg
imported from: obi.owl

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
subclass of: data about an ontology part
editor preferred label: obsolescence reason specification
has curation status: pending final vetting
textual definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

textual entity
type: Class
subclass of: information content entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: metadata incomplete
textual 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.
definition editor: PERSON: Lawrence Hunter
alternative term: text
imported from: obi.owl

institutional identification
type: Class
subclass of: textual entity
editor preferred label: institutional identification
example of usage: University of Colorado Denver School of Medicine
has curation status: pending final vetting
textual definition: A textual entity intended to identify a particular institution
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: metadata complete
textual definition: A collection of information content entities intended to be understood together as a whole
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographic location
has curation status: metadata incomplete
textual 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 https://github.com/information-artifact-ontology/IAO/issues/59
imported from: obi.owl

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
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: pending final vetting
textual definition: a planned process in which a document is created or added to by including the specified input in it.
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
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
imported from: obi.owl

Mus musculus
type: Class
subclass of: Murinae
subclass of: Restriction
  on property: is animal model for disease
  some values from: brucellosis
subclass of: Restriction
  on property: is animal model for disease
  some values from: tuberculosis
subclass of: Restriction
  on property: is animal model for disease
  some values from: Influenza A virus
subclass of: Restriction
  on property: is animal model for disease
  some values from: Influenza B virus
subclass of: Restriction
  on property: is animal model for disease
  some values from: Influenza C virus
subclass of: Restriction
  on property: is animal model for disease
  some values from: Human immunodeficiency virus
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:85055
database_cross_reference: GC_ID:1
has exact synonym: house mouse
has exact synonym: mouse
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Mus muscaris
has_related_synonym: mice C57BL/6xCBA/CaJ hybrid

Rattus
type: Class
subclass of: Murinae
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has exact synonym: rat
has exact synonym: rats
has_obo_namespace: ncbi_taxonomy

Cavia porcellus
type: Class
subclass of: Hystricomorpha
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:84274
database_cross_reference: GC_ID:1
has exact synonym: domestic guinea pig
has exact synonym: guinea pig
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Cavia aperea porcellus
has_related_synonym: Cavia cobaya
has_related_synonym: Cavia cobya

Chinchillidae
type: Class
subclass of: Hystricomorpha
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has exact synonym: chinchillas
has exact synonym: chinchillas and viscachas
has_obo_namespace: ncbi_taxonomy

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl
imported from: obi.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vira
has_related_synonym: Viridae
has_related_synonym: viruses

Orthomyxoviridae
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Influenza A virus
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_broad_synonym: FLUAV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Human Influenza A Virus
has_related_synonym: Influenza virus type A
has_related_synonym: influenza A virus INF A

Influenza B virus
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_broad_synonym: FLUBV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Influenza virus type B

Influenza C virus
type: Class
subclass of: Orthomyxoviridae
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:186678
has_broad_synonym: FLUCV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Influenza C viruses
has_related_synonym: Influenza virus type C

Lentivirus
type: Class
subclass of: Viruses
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Lentivirinae

Primate lentivirus group
type: Class
subclass of: Lentivirus
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Primate immunodeficiency viruses

Brucellaceae
type: Class
subclass of: Rhizobiales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Proteobacteria
type: Class
subclass of: Bacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11321122
database_cross_reference: PMID:11542017
database_cross_reference: PMID:11837318
database_cross_reference: PMID:16280474
database_cross_reference: PMID:26654112
has exact synonym: purple bacteria
has exact synonym: purple bacteria and relatives
has exact synonym: purple non-sulfur bacteria
has exact synonym: purple photosynthetic bacteria
has exact synonym: purple photosynthetic bacteria and relatives
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Alphaproteobacteraeota
has_related_synonym: proteobacteria

Human immunodeficiency virus
type: Class
subclass of: unclassified Primate lentivirus group
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_broad_synonym: HIV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: AIDS virus

Boreoeutheria
type: Class
subclass of: Vertebrata <Metazoa>
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11743200
database_cross_reference: PMID:11791233
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Boreotheria

Simian-Human immunodeficiency virus 1
type: Class
subclass of: Simian-Human immunodeficiency virus
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Actinobacteria <class>
type: Class
subclass of: Actinobacteria <phylum>
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
has_alternative_id: NCBITaxon:85003
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10028260
database_cross_reference: PMID:11155976
database_cross_reference: PMID:11321122
database_cross_reference: PMID:19244447
database_cross_reference: PMID:28840812
has exact synonym: Actinobacteria
has exact synonym: high G+C Gram-positive bacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Actinomycetes
has_related_synonym: High GC gram-positive bacteria
has_related_synonym: high GC Gram+

Mycobacteriaceae
type: Class
subclass of: Corynebacteriales
imported from: ncbitaxon.owl
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19244447
database_cross_reference: PMID:29497402
has_obo_namespace: ncbi_taxonomy

Mycobacterium
type: Class
subclass of: Mycobacteriaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1380284
database_cross_reference: PMID:1581193
database_cross_reference: PMID:16014496
database_cross_reference: PMID:1883713
database_cross_reference: PMID:2275850
database_cross_reference: PMID:29497402
database_cross_reference: PMID:7547284
database_cross_reference: PMID:7547304
database_cross_reference: PMID:7907223
database_cross_reference: PMID:8863452
has_obo_namespace: ncbi_taxonomy

Mycobacterium tuberculosis
type: Class
subclass of: Mycobacterium tuberculosis complex
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:29205127
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus tuberculosis
has_related_synonym: Bacterium tuberculosis
has_related_synonym: Mycobacterium tuberculosis typus humanus
has_related_synonym: Mycobacterium tuberculosis var. hominis

Terrabacteria group
type: Class
subclass of: Bacteria
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
database_cross_reference: PMID:18988685
database_cross_reference: PMID:23851394
has_obo_namespace: ncbi_taxonomy

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl
imported from: obi.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11542017
database_cross_reference: PMID:11542087
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:270744
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: PMID:9336922
has exact synonym: eubacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Actinobacteria <phylum>
type: Class
subclass of: Terrabacteria group
imported from: ncbitaxon.owl
has_rank: NCBITaxon phylum
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11837318
database_cross_reference: PMID:16280504
database_cross_reference: PMID:26654112
has exact synonym: Actinobacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Actinobacteraeota
has_related_synonym: actinobacteria

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl
imported from: obi.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11541975
database_cross_reference: PMID:11542064
database_cross_reference: PMID:11542149
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:25527841
database_cross_reference: PMID:270744
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: PMID:9336922
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Archaebacteria
has_related_synonym: Mendosicutes
has_related_synonym: Metabacteria
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: archaea
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Brucella melitensis bv. 1 str. 16M
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11756688
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Brucella melitensis 16M
has_related_synonym: Brucella melitensis ATCC 23456
has_related_synonym: Brucella melitensis str. 16M
has_related_synonym: Brucella melitensis str. ATCC 23456

Brucella
type: Class
subclass of: Brucellaceae
imported from: ncbitaxon.owl
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:28066370
database_cross_reference: PMID:8573514
has_obo_namespace: ncbi_taxonomy

Brucella abortus
type: Class
subclass of: Brucella
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has exact synonym: Brucella melitensis bv. Abortus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacterium abortus
has_related_synonym: Brucella melitensis biovar Abortus

Eukaryota
type: Class
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl
imported from: obi.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
has exact synonym: eucaryotes
has exact synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Bovinae
type: Class
subclass of: Boreoeutheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Alphaproteobacteria
type: Class
subclass of: Proteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11541974
database_cross_reference: PMID:11837318
database_cross_reference: PMID:16166687
database_cross_reference: PMID:16403855
database_cross_reference: PMID:19060069
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Alphabacteria
has_related_synonym: Proteobacteria alpha subdivision
has_related_synonym: Purple bacteria, alpha subdivision
has_related_synonym: a-proteobacteria
has_related_synonym: alpha proteobacteria
has_related_synonym: alpha subdivision
has_related_synonym: alpha subgroup

Euarchontoglires
type: Class
subclass of: Boreoeutheria
imported from: ncbitaxon.owl
has_rank: NCBITaxon superorder
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11214319
database_cross_reference: PMID:12082125
database_cross_reference: PMID:12878460
database_cross_reference: PMID:15522813
has_obo_namespace: ncbi_taxonomy

Glires
type: Class
subclass of: Euarchontoglires
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11214319
database_cross_reference: PMID:12082125
database_cross_reference: PMID:15522813
has exact synonym: Rodents and rabbits
has_obo_namespace: ncbi_taxonomy

Simiiformes
type: Class
subclass of: Primates
imported from: ncbitaxon.owl
has_rank: NCBITaxon infraorder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anthropoidea

Hystricomorpha
type: Class
subclass of: Rodentia
imported from: ncbitaxon.owl
has_rank: NCBITaxon suborder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Hystricognathi

Mycobacterium bovis BCG
type: Class
subclass of: Mycobacterium tuberculosis complex
imported from: ncbitaxon.owl
has_broad_synonym: BCG
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Mycobacterium tuberculosis var. bovis BCG
has_related_synonym: bacillus Calmette-Guerin
has_related_synonym: bacillus Calmette-Guerin BCG

Rhizobiales
type: Class
subclass of: Alphaproteobacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16403855
database_cross_reference: PMID:1854635
has exact synonym: rhizobacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Rhizobiaceae group
has_related_synonym: alpha-2 proteobacteria

Brucella abortus 2308
type: Class
subclass of: Brucella abortus
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16299333
database_cross_reference: PMID:20462421
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Brucella melitensis biovar Abortus 2308

Murinae
type: Class
subclass of: Rodentia
imported from: ncbitaxon.owl
has_rank: NCBITaxon subfamily
has_alternative_id: NCBITaxon:109679
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Bubalus bubalis bubalis
type: Class
subclass of: Bovinae
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Brucella abortus S19
type: Class
subclass of: Brucella abortus
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:11
has exact synonym: Brucella abortus str. S19
has exact synonym: Brucella abortus strain S19
has_obo_namespace: ncbi_taxonomy

Simian-Human immunodeficiency virus
type: Class
subclass of: unclassified Primate lentivirus group
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_broad_synonym: HIV
has_broad_synonym: SHIV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: SIV/HIV

unclassified Primate lentivirus group
type: Class
subclass of: Primate lentivirus group
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Vertebrata <Metazoa>
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has exact synonym: Vertebrata
has exact synonym: vertebrates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: vertebrates

Mycobacterium tuberculosis complex
type: Class
subclass of: Mycobacterium
imported from: ncbitaxon.owl
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
database_cross_reference: PMID:15243089
database_cross_reference: PMID:29205127
has exact synonym: Mycobacterium complex
has_obo_namespace: ncbi_taxonomy

Corynebacteriales
type: Class
subclass of: Actinobacteria <class>
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
has_alternative_id: NCBITaxon:1761
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11837321
database_cross_reference: PMID:1736962
database_cross_reference: PMID:19244447
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Corynebacterineae

Primates
type: Class
subclass of: Euarchontoglires
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has exact synonym: primate
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Primata
has_related_synonym: primates

Platyrrhini
type: Class
subclass of: Simiiformes
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon parvorder
database_cross_reference: GC_ID:1
has exact synonym: New World monkeys
has exact synonym: monkey
has exact synonym: monkeys
has_obo_namespace: ncbi_taxonomy

Homo sapiens
type: Class
subclass of: Simiiformes
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: human
has exact synonym: man
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Home sapiens
has_related_synonym: Homo sampiens
has_related_synonym: Homo sapeins
has_related_synonym: Homo sapian
has_related_synonym: Homo sapians
has_related_synonym: Homo sapien
has_related_synonym: Homo sapience
has_related_synonym: Homo sapiense
has_related_synonym: Homo sapients
has_related_synonym: Homo sapines
has_related_synonym: Homo spaiens
has_related_synonym: Homo spiens
has_related_synonym: Humo sapiens

Bison bison
type: Class
subclass of: Bovinae
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: American bison
has exact synonym: Bison
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bos (Bison) bison

Oryctolagus cuniculus
type: Class
subclass of: Glires
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:34833
has_alternative_id: NCBITaxon:9985
database_cross_reference: GC_ID:1
has exact synonym: European rabbit
has exact synonym: Japanese white rabbit
has exact synonym: domestic rabbit
has exact synonym: rabbit
has exact synonym: rabbits
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Lepus cuniculus

Rodentia
type: Class
subclass of: Glires
imported from: ncbitaxon.owl
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has exact synonym: rodent
has_obo_namespace: ncbi_taxonomy
has_related_synonym: rodents

adverse event
type: Class
subclass of: pathological bodily process
subclass of: Restriction
  on property: preceded_by
  some values from: medical intervention
textual definition: a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
editor note: Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
editor note: YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
editor note: YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
editor note: YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
editor note: YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
editor note: YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
editor note: YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
definition editor: Yongqun He
alternative term: AE
alternative term: adverse reaction
definition source: WEB: http://en.wikipedia.org/wiki/Adverse_event
definition source: WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
imported from: OAE: Ontology of Adverse Events
comment: The OAE official website is: http://www.oae-ontology.org/.

medical intervention
type: Class
subclass of: planned process
textual definition: medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
editor note: The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
definition editor: YH
definition source: WEB: http://wiki.answers.com/Q/What_is_medical_intervention
imported from: OAE: Ontology of Adverse Events

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
textual definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: vo.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
textual definition: Is a material entity that is created or changed during material processing.
definition editor: PERSON: Alan Ruttenberg
imported from: obi.owl

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
textual definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
definition editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
ISA alternative term: study

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
editor preferred label: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: ready for release
textual definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
textual 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.
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 editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

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

diagnosis textual entity
type: Class
subclass of: textual entity
editor preferred label: diagnosis textual entity
has curation status: metadata incomplete
textual definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
definition editor: Jennifer Fostel
imported from: obi.owl

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
textual 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.
definition editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: obi.owl
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…

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

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
textual 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: ready for release
textual 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 editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl
ISA alternative term: study protocol

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: conclusion based on data
editor preferred label: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: ready for release
textual 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
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters
imported from: obi.owl

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred label: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: ready for release
textual definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
definition editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch
imported from: obi.owl

hypothesis driven investigation
type: Class
subclass of: investigation
editor preferred label: hypothesis driven investigation
has curation status: pending final vetting
textual definition: is an investigation with the goal to test one or more hypothesis
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

hypothesis generating investigation
type: Class
subclass of: investigation
editor preferred label: hypothesis generating investigation
has curation status: pending final vetting
textual definition: is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

contain function
type: Class
subclass of: function
editor preferred label: contain function
example of usage: A syringe, a beaker
has curation status: ready for release
textual definition: A contain function is a function to constrain a material entities location in space
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: ready for release
textual definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
definition editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
textual definition: an objective specifiction that creates an specific output object from input materials.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

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: study design
subclass of: planned process
editor preferred label: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: ready for release
textual definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: obi.owl

container
type: Class
equivalent class: Restriction
  on property: has function
  some values from: contain function
subclass of: device
editor preferred label: container
has curation status: metadata incomplete
textual definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
definition editor: PERSON: Bjoern Peters
imported from: obi.owl

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
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
textual definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has curation status: ready for release
textual definition: An information content entity that is inferred from data.
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
definition editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
textual definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: ready for release
textual definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

animal cage
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
editor preferred label: animal cage
example of usage: PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
has curation status: ready for release
textual definition: a processed material which has the function to define a bounded habitat which is amenable to keeping animals.
definition editor: PERSON: Phillippe Rocca-Serra
alternative term: laboratory cage
definition source: OBI biomaterial branch
imported from: obi.owl

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred label: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: ready for release
textual definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
definition editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

clinical history
type: Class
subclass of: information content entity
editor preferred label: clinical history
textual definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
imported from: obi.owl
imported from: ogms.owl

bodily process
type: Class
subclass of: process
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:53:49Z
imported from: OAE: Ontology of Adverse Events
imported from: ogms.owl

pathological bodily process
type: Class
subclass of: bodily process
textual definition: A bodily process that is clinically abnormal.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:54:29Z
imported from: OAE: Ontology of Adverse Events
imported from: ogms.owl

disease course
type: Class
subclass of: biological_process
editor preferred label: disease course
textual definition: The totality of all processes through which a given disease instance is realized.
curator note: replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role'
imported from: obi.owl
imported from: ogms.owl

diagnosis
type: Class
subclass of: data item
editor preferred label: diagnosis
textual definition: The representation of a conclusion of a diagnostic process.
imported from: obi.owl
imported from: ogms.owl

treatment
type: Class
subclass of: planned process
editor preferred label: treatment
textual definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
imported from: obi.owl
imported from: ogms.owl

laboratory animal
type: Class
equivalent class: Restriction
  on property: has role
  some values from: laboratory animal role
subclass of: organism
subclass of: Restriction
  on property: has role
  some values from: laboratory animal role
textual definition: An animal organism that is used as an animal model of a human or animal disease in translational and biomedical research.
definition editor: Oliver He
alternative term: animal model
alternative term: laboratory animal model
definition source: https://en.wikipedia.org/wiki/Comparative_medicine

laboratory animal role
type: Class
subclass of: role
textual definition: a role that inheres in an animal that is used as a model for human or animal research.
definition editor: Oliver He
alternative term: animal model role
definition source: https://en.wikipedia.org/wiki/Comparative_medicine

laboratory animal investigation
type: Class
subclass of: investigation
textual definition: An investigation that uses a non-human laboratory animal in a study
definition editor: Oliver He
alternative term: animal experimentation
alternative term: animal research
alternative term: animal testing
definition source: https://en.wikipedia.org/wiki/Animal_testing

The laboratory animal Three Rs principle
type: Class
subclass of: action specification
textual definition: First described by W. M. S. Russell and R. L. Burch in 1959, the Three Rs (3Rs) in relation to science are guiding principles for more ethical use of animals in testing. The three Rs mean Replacement, Reduction, and Refinement.
definition editor: Oliver He
alternative term: 3Rs
definition source: Russell, W.M.S. and Burch, R.L., (1959). The Principles of Humane Experimental Technique, Methuen, London. ISBN 0900767782.
definition source: https://en.wikipedia.org/wiki/The_Three_Rs

Replacement principle
type: Class
subclass of: The laboratory animal Three Rs principle
subclass of: Restriction
  on property: is about
  some values from: laboratory animal replacement
textual definition: As one of the three Rs, the Replacement principle suggests the usage of methods to avoid or replace the use of animals in research
definition editor: Oliver He
definition source: Russell, W.M.S. and Burch, R.L., (1959). The Principles of Humane Experimental Technique, Methuen, London. ISBN 0900767782.
definition source: https://en.wikipedia.org/wiki/The_Three_Rs

Reduction principle
type: Class
subclass of: The laboratory animal Three Rs principle
subclass of: Restriction
  on property: is about
  some values from: laboratory animal reduction
textual definition: As one of the three Rs, the Reduction principle suggests the usage of methods to enable researchers to obtain comparable levels of information from fewer animals, or to obtain more information from the same number of animals.
definition editor: Oliver He
definition source: Russell, W.M.S. and Burch, R.L., (1959). The Principles of Humane Experimental Technique, Methuen, London. ISBN 0900767782.
definition source: https://en.wikipedia.org/wiki/The_Three_Rs

Refinement principle
type: Class
subclass of: The laboratory animal Three Rs principle
subclass of: Restriction
  on property: is about
  some values from: laboratory animal refinement
textual definition: As one of the three Rs, the Refinement principle proposes the usage of methods to alleviate or minimize potential pain, suffering or distress, and enhance animal welfare for the animals used
definition editor: Oliver He
definition source: Russell, W.M.S. and Burch, R.L., (1959). The Principles of Humane Experimental Technique, Methuen, London. ISBN 0900767782.
definition source: https://en.wikipedia.org/wiki/The_Three_Rs

mouse cage
type: Class
subclass of: animal cage
textual definition: An animal cage that keeps mouse
definition editor: Oliver He

laboratory animal for human disease research
type: Class
subclass of: laboratory animal
textual definition: a laboratory animal that is used for human disease research
definition editor: Oliver He
definition source: https://www.sciencedirect.com/book/9780124158948/animal-models-for-the-study-of-human-disease

laboratory animal for tuberculosis research
type: Class
equivalent class: Restriction
  on property: is animal model for disease
  some values from: tuberculosis
subclass of: laboratory animal for human disease research
subclass of: Restriction
  on property: is animal model for disease
  some values from: tuberculosis
textual definition: a laboratory animal that is used for tuberculosis disease research
definition editor: Oliver He
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825961/

laboratory animal for zoonotic disease research
type: Class
subclass of: laboratory animal for human disease research
textual definition: a laboratory animal that is used for zoonotic disease research

laboratory animal for brucellosis research
type: Class
equivalent class: Restriction
  on property: is animal model for disease
  some values from: brucellosis
subclass of: laboratory animal for zoonotic disease research
subclass of: Restriction
  on property: is animal model for disease
  some values from: brucellosis
textual definition: a laboratory animal that is used for zoonotic brucellosis research
definition editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Brucellosis

laboratory animal for HIV research
type: Class
equivalent class: Restriction
  on property: is animal model for disease
  some values from: Human immunodeficiency virus
subclass of: laboratory animal for human disease research
subclass of: Restriction
  on property: is animal model for disease
  some values from: Human immunodeficiency virus
textual definition: a laboratory animal that is used for HIV/AIDS research
definition editor: Oliver He
definition source: https://www.sciencedirect.com/science/article/pii/B9780123694089000251

immune response of mouse and not human
type: Class
equivalent class: Class
  intersection of: immune response
  intersection of: Restriction
    on property: occurs in
    some values from: Mus musculus
  intersection of: Restriction
    on property: absent in process
    some values from: Homo sapiens
subclass of: immune response
subclass of: Restriction
  on property: occurs in
  some values from: Mus musculus
subclass of: Restriction
  on property: absent in process
  some values from: Homo sapiens
definition source: http://www.jimmunol.org/content/172/5/2731

immune response of human and not mouse
type: Class
equivalent class: Class
  intersection of: immune response
  intersection of: Restriction
    on property: occurs in
    some values from: Homo sapiens
  intersection of: Restriction
    on property: absent in process
    some values from: Mus musculus
subclass of: immune response
subclass of: Restriction
  on property: occurs in
  some values from: Homo sapiens
subclass of: Restriction
  on property: absent in process
  some values from: Mus musculus
definition source: http://www.jimmunol.org/content/172/5/2731

protein in mouse but not human
type: Class
equivalent class: Class
  intersection of: protein
  intersection of: Restriction
    on property: absent in location
    some values from: Homo sapiens
  intersection of: Restriction
    on property: located in
    some values from: Mus musculus
subclass of: protein
definition source: http://www.jimmunol.org/content/172/5/2731

protein in human but not mouse
type: Class
equivalent class: Class
  intersection of: protein
  intersection of: Restriction
    on property: absent in location
    some values from: Mus musculus
  intersection of: Restriction
    on property: located in
    some values from: Homo sapiens
subclass of: protein
definition source: http://www.jimmunol.org/content/172/5/2731

animal euthanasia
type: Class
subclass of: planned process
textual definition: A planned process that intentionally puts an animal to death or allows to die by withholding extreme medical measures
alternative term: euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia

euthanasia best practice
type: Class
subclass of: animal euthanasia
textual definition: An euthanasia process that follows the best practice principle
alternative term: animal euthanasia best practice

intravenous anesthetic euthanasia
type: Class
subclass of: animal euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intravenous_Anesthetic

inhalant euthanasia
type: Class
subclass of: animal euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Inhalants

cervical dislocation
type: Class
subclass of: animal euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Cervical_dislocation

intracardiac injection euthanasia
type: Class
subclass of: animal euthanasia
alternative term: IC injection
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intracardiac_or_intraperitoneal_injection

intraperitoneal injection euthanasia
type: Class
subclass of: animal euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intracardiac_or_intraperitoneal_injection

pentobarbital intracardiac injection euthanasia
type: Class
subclass of: intracardiac injection euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intracardiac_or_intraperitoneal_injection

shooting euthanasia
type: Class
subclass of: animal euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Shooting

firearm shooting euthanasia
type: Class
subclass of: shooting euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Shooting

captive bolt gun shooting euthanasia
type: Class
subclass of: shooting euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Shooting

isoflurane inhalant euthanasia
type: Class
subclass of: inhalant euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Inhalants

sevoflurane inhalant euthanasia
type: Class
subclass of: inhalant euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Inhalants

carbon dioxide inhalant euthanasia
type: Class
subclass of: inhalant euthanasia
alternative term: CO2 inhalant euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Inhalants

barbiturate intravenous anesthetic euthanasia
type: Class
subclass of: intravenous anesthetic euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intravenous_Anesthetic

somulose intravenous anesthetic euthanasia
type: Class
subclass of: intravenous anesthetic euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intravenous_Anesthetic

tributame intravenous anesthetic euthanasia
type: Class
subclass of: intravenous anesthetic euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Intravenous_Anesthetic

carbon monoxide inhalant euthanasia
type: Class
subclass of: inhalant euthanasia
alternative term: CO2 inhalant euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Inhalants

nitrogen inhalant euthanasia
type: Class
subclass of: inhalant euthanasia
alternative term: CO2 inhalant euthanasia
definition source: https://en.wikipedia.org/wiki/Animal_euthanasia#Inhalants

animal welfare
type: Class
subclass of: planned process
textual definition: A planned process that supports the well-being of nonhuman animal
definition source: https://en.wikipedia.org/wiki/Animal_welfare

animal welfare act
type: Class
subclass of: action specification
subclass of: Restriction
  on property: is about
  some values from: animal welfare
definition source: https://en.wikipedia.org/wiki/Animal_welfare

laboratory animal welfare act
type: Class
subclass of: animal welfare act
subclass of: Restriction
  on property: is about
  some values from: animal welfare
definition source: https://en.wikipedia.org/wiki/Animal_welfare

USA animal welfare act
type: Class
subclass of: animal welfare act

UK animal welfare act
type: Class
subclass of: animal welfare act

Ireland animal welfare act
type: Class
subclass of: animal welfare act

Indian animal welfare act
type: Class
subclass of: animal welfare act
definition source: https://en.wikipedia.org/wiki/Animal_welfare

laboratory animal reduction
type: Class
subclass of: planned process

laboratory animal refinement
type: Class
subclass of: planned process

laboratory animal replacement
type: Class
subclass of: planned process

United Nations animal welfare act
type: Class
subclass of: animal welfare act
definition source: https://en.wikipedia.org/wiki/Animal_welfare

adverse event in animal
type: Class
subclass of: adverse event

Institutional Animal Care and Use Committee
type: Class
subclass of: organization
alternative term: IACUC
definition source: https://www.nabr.org/animal-welfare-2/animal-welfare-in-practice/functions-of-the-iacuc/

laboratory animal for plague research
type: Class
subclass of: laboratory animal for zoonotic disease research
textual definition: a laboratory animal that is used for study of zoonotic plague disease, which is caused by the bacterium Yersinia pestis
definition editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Plague_(disease)

lab animal equipment sanitation
type: Class
subclass of: sanitation

rodent cage sanitation
type: Class
subclass of: lab animal equipment sanitation

sanitation of rodent cage part
type: Class
subclass of: lab animal equipment sanitation

sanitation of rodent cage water bottle
type: Class
subclass of: sanitation of rodent cage part

ventilated rodent cage sanitation
type: Class
subclass of: rodent cage sanitation

laboratory animal equipment
type: Class
subclass of: material entity

rodent cage
type: Class
subclass of: laboratory animal equipment

rodent cage part
type: Class
subclass of: laboratory animal equipment

lab rodent breeding cage
type: Class
subclass of: rodent cage

PP rodent laboratory cage
type: Class
subclass of: rodent cage
definition editor: Oliver He
alternative term: Polypropylene Rodent Cage
definition source: https://www.alibaba.com/product-detail/PP-Rodent-laboratory-cages_60806220382.html

laboratory animal for human coronavirus research
type: Class
subclass of: laboratory animal for zoonotic disease research

lab animal of human disease pathogenesis
type: Class
subclass of: laboratory animal for human disease research

lab animal for human vaccine study
type: Class
subclass of: laboratory animal for human disease research

lab animal of human vaccine efficacy study
type: Class
subclass of: lab animal for human vaccine study

lab animal for human vaccine safety study
type: Class
subclass of: lab animal for human vaccine study

lab animal of human tuberculosis pathogenesis
type: Class
subclass of: lab animal of human disease pathogenesis
subclass of: Restriction
  on property: is animal model for disease
  some values from: tuberculosis

lab animal of human TB vaccine efficacy study
type: Class
subclass of: lab animal of human vaccine efficacy study
subclass of: Restriction
  on property: is animal model for disease
  some values from: tuberculosis

lab animal of human brucellosis vaccine efficacy study
type: Class
subclass of: lab animal of human vaccine efficacy study
subclass of: Restriction
  on property: is animal model for disease
  some values from: brucellosis

lab animal for human brucellosis vaccine safety study
type: Class
subclass of: lab animal for human vaccine safety study
subclass of: Restriction
  on property: is animal model for disease
  some values from: brucellosis

lab animal of human TB vaccine safety study
type: Class
subclass of: lab animal for human vaccine safety study
subclass of: Restriction
  on property: is animal model for disease
  some values from: tuberculosis

lab animal for COVID-19 vaccine study
type: Class
subclass of: lab animal for human vaccine study

lab animal for COVID-19 research
type: Class
subclass of: laboratory animal for human disease research

sanitation
type: Class
subclass of: process
textual definition: A public health process that involves clean drinking water and adequate treatment and disposal of human and animal excreta and sewage.
definition source: https://en.wikipedia.org/wiki/Sanitation
imported from: OPMI: Ontology of Precision Medicine and Investigation

protein
type: Class
subclass of: material entity
textual definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
imported from: pr.owl
has_obo_namespace: protein
id: PR:000000001
comment: Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].

caspase-10
type: Class
subclass of: protein
subclass of: Restriction
  on property: absent in location
  some values from: Mus musculus
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens
textual definition: A caspase-8-like protease that is a translation product of the human CASP10 gene or a 1:1 ortholog thereof.
imported from: pr.owl
database_cross_reference: IUPHARobj:1626
database_cross_reference: PIRSF:PIRSF500655
has exact synonym: CASP-10
has exact synonym: CASP10
has exact synonym: FAS-associated death domain protein interleukin-1B-converting enzyme 2
has exact synonym: FLICE2
has exact synonym: ICE-like apoptotic protease 4
has exact synonym: apoptotic protease Mch-4
has_obo_namespace: protein
has_related_synonym: MCH4
id: PR:000002310
comment: Category=gene. Not found in mouse.

example to be eventually removed
type: NamedIndividual
type: curation status specification

failed exploratory term
type: Thing
type: NamedIndividual
type: obsolescence reason specification
textual definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
definition editor: Person:Alan Ruttenberg

metadata complete
type: Thing
type: NamedIndividual
type: curation status specification
textual definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: Thing
type: NamedIndividual
type: curation status specification
textual definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release
definition editor: PERSON:Alan Ruttenberg

ready for release
type: Thing
type: NamedIndividual
type: curation status specification
has curation status: pending final vetting
textual definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: Thing
type: NamedIndividual
type: curation status specification
textual definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: Thing
type: NamedIndividual
type: curation status specification
textual definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: Thing
type: NamedIndividual
type: curation status specification
textual definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

placeholder removed
type: Thing
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
textual definition: Terms with this status should eventually replaced with a term from another ontology.
definition editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
textual definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
definition editor: Alan Ruttenberg
definition source: group:OBI

American Veterinary Medical Association
type: NamedIndividual
type: organization
alternative term: AVMA
definition source: https://www.avma.org

An Act against Plowing by the Tayle, and pulling the Wooll off living Sheep
type: NamedIndividual
type: Ireland animal welfare act
definition source: https://en.wikipedia.org/wiki/An_Act_against_Plowing_by_the_Tayle,_and_pulling_the_Wooll_off_living_Sheep

Animal Welfare Act 2006
type: NamedIndividual
type: USA animal welfare act
definition source: https://en.wikipedia.org/wiki/Animal_Welfare_Act_2006

Cruelty to Animals Act 1835
type: NamedIndividual
type: Ireland animal welfare act
definition source: https://en.wikipedia.org/wiki/Cruelty_to_Animals_Act_1835

Protection of Animals Act 1911
type: NamedIndividual
type: UK animal welfare act
definition source: https://en.wikipedia.org/wiki/Protection_of_Animals_Act_1911

Animal Welfare Act of 1966
type: NamedIndividual
type: USA animal welfare act

Prevention of Cruelty to Animals Act
type: NamedIndividual
type: Indian animal welfare act
definition source: https://en.wikipedia.org/wiki/Prevention_of_Cruelty_to_Animals_Act

Universal Declaration on Animal Welfare
type: NamedIndividual
type: United Nations animal welfare act
alternative term: UDAW
definition source: https://en.wikipedia.org/wiki/Universal_Declaration_on_Animal_Welfare

axiom holds for all times
type: NamedIndividual
textual definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

iao.owl
type: NamedIndividual
default language: en
imported from: bfo.owl
imported from: externalByHand.owl
imported from: iao-main.owl
imported from: iao.owl
imported from: import-OBO.owl
imported from: obsolete.owl
imported from: ontology-metadata.owl
imported from: annotations.owl
imported from: bfo-axioms.owl
imported from: bfo-classes-minimal.owl
imported from: core.owl
Contributor: Adam Goldstein
Contributor: Alan Ruttenberg
Contributor: Albert Goldfain
Contributor: Barry Smith
Contributor: Bjoern Peters
Contributor: Carlo Torniai
Contributor: Chris Mungall
Contributor: Chris Stoeckert
Contributor: Christian A. Boelling
Contributor: Darren Natale
Contributor: David Osumi-Sutherland
Contributor: Gwen Frishkoff
Contributor: Holger Stenzhorn
Contributor: James A. Overton
Contributor: James Malone
Contributor: Jennifer Fostel
Contributor: Jie Zheng
Contributor: Jonathan Rees
Contributor: Larisa Soldatova
Contributor: Lawrence Hunter
Contributor: Mathias Brochhausen
Contributor: Matt Brush
Contributor: Melanie Courtot
Contributor: Michel Dumontier
Contributor: Paolo Ciccarese
Contributor: Pat Hayes
Contributor: Philippe Rocca-Serra
Contributor: Randy Dipert
Contributor: Ron Rudnicki
Contributor: Satya Sahoo
Contributor: Sivaram Arabandi
Contributor: Werner Ceusters
Contributor: William Duncan
Contributor: William Hogan
Contributor: Yongqun (Oliver) He
license: http://creativecommons.org/licenses/by/4.0/
comment: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
comment: IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
comment: IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
comment: The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html
comment: This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner

obi.owl
type: NamedIndividual
default language: en
OBO foundry unique label: Ontology for Biomedical Investigations
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
creator: Chris Stoeckert
creator: Chris Taylor
creator: Christian Bolling
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James A. Overton
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
creator: Philip Lord
creator: Philippe Rocca-Serra
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
date: 2009-07-31
description: 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.
Format: OWL-DL
subject: An ontology for the annotation of biomedical and functional genomics experiments.
license: http://creativecommons.org/licenses/by/4.0/
comment: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
version info: 2018-08-27

dron.owl
comment: An ontology of drugs.
creator: Josh Hanna
creator: William Hogan
comment: DrOn contains content developed by the National Library of Medicine in RxNorm. In creating DrOn, we have used RxNorm content only with SAB = RXNORM.
license: https://creativecommons.org/licenses/by/3.0/
creator: Eric Joseph
comment: When citing DrOn, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/dron.owl. When referencing a specific component of the DrOn, such as a class, object property, annotation property, or individual, use the Uniform Resource Identifier (URI) of that component.
creator: Mathias Brochhausen

envo.owl
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/chebi_import.owl>))) [Axioms: 2434 Logical Axioms: 1036]
default-namespace: ENVO
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/ro_import.owl>))) [Axioms: 1192 Logical Axioms: 302]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>))) [Axioms: 21 Logical Axioms: 2]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/go_import.owl>))) [Axioms: 270 Logical Axioms: 76]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/pco_import.owl>))) [Axioms: 21 Logical Axioms: 3]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/pato_import.owl>))) [Axioms: 1362 Logical Axioms: 337]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/obi_import.owl>))) [Axioms: 50 Logical Axioms: 12]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>))) [Axioms: 79 Logical Axioms: 12]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/clo_import.owl>))) [Axioms: 34 Logical Axioms: 8]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/fao_import.owl>))) [Axioms: 4 Logical Axioms: 0]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/ncbitaxon_import.owl>))) [Axioms: 542 Logical Axioms: 123]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/flopo_import.owl>))) [Axioms: 1536 Logical Axioms: 352]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/bfo_import.owl>))) [Axioms: 92 Logical Axioms: 35]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/uberon_import.owl>))) [Axioms: 24081 Logical Axioms: 4670]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/po_import.owl>))) [Axioms: 151 Logical Axioms: 18]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>))) [Axioms: 45 Logical Axioms: 6]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/omp_import.owl>))) [Axioms: 47 Logical Axioms: 11]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/foodon_import.owl>))) [Axioms: 63 Logical Axioms: 7]
comment: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ Please see www.environmentontology.org for more information and citations.
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>))) [Axioms: 131 Logical Axioms: 22]

OAE: Ontology of Adverse Events
creator: Desikan Jagannathan
subject: An ontology for the annotation of the adverse event domain.
Contributor: Elizabeth Blair
creator: "Asiyah" Yu Lin
creator: Abra Guo
Contributor: Sydni Joubran
version info: Vision Release; 1.2.17
Format: OWL-DL
editor note: Product version
Contributor: Darrell R. Abernethy
creator: Sirarat Sarntivijai
creator: Ling Wan
creator: Rebecca Racz
creator: Shelley Zhang
creator: Liwei Wang
creator: Meiu Wong
description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
creator: Kevin Mo
creator: Yongqun "Oliver" He (YH)
Contributor: Luca Toldo
creator: Noemi Garg
Contributor: Keith Burkhart
creator: Edison Ong
Contributor: Mathias Brochhausen
Contributor: Izabela Birsanescu
creator: Zuoshuang "Allen" Xiang
creator: Barry Smith
creator: Bingjian Yang
license: http://creativecommons.org/licenses/by/3.0/
creator: Qingping Liu
creator: Jiangan Xie
date: 2019-2-15
creator: Sydni Joubran
creator: Kelly Yang
creator: David Ameriguian

ogms.owl
creator: Daniel Merico
creator: Werner Ceusters
creator: Bill Hogan
creator: Albert Goldfain
comment: This ontology is in early development. Expect it to change.
version info: 2011-09-20
creator: Alan Ruttenberg
creator: Sivaram Arabandi
creator: Lindsay Cowell
date: 2009-08-07
creator: Richard Scheuermann
creator: Cornelius Rosse
creator: Anand Kumar
comment: The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is always available at http://purl.obolibrary.org/obo/ogms.owl This is version 2011-09-20 aka '0.9' http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl The OGMS developer site is http://code.google.com/p/ogms/ The discussion group is http://groups.google.com/group/ogms-discuss If you are interested in participating in the development of OGMS, please send email to albertgoldfain@gmail.com. Be sure to include a google-account username with your request (this will be the username associated with a gmail address).
creator: Barry Smith

The Ontology of Medically Related Social Entities
comment: This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
creator: William Hogan
version info: 2017-06-08
creator: Amanda Hicks
creator: Mathias Brochhausen
creator: Swetha Garimalla
Contributor: Daniel Welch
creator: Shariq Tariq

OPMI: Ontology of Precision Medicine and Investigation
creator: Yongqun "Oliver" He (YH)
creator: Jie Zheng
version info: Vision Release: 1.0.48
creator: Jennifer Schaub
subject: OPMI subject: Precision medicine and related investigations
Format: OWL-DL
Contributor: Sean Mooney
creator: Fred Dowd
date: 2-17-2019
description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.
Contributor: Christopher Park
Contributor: John O'toole
Contributor: Becky Steck
creator: Hong Yu