TSO: Transportation System Ontology
type: Ontology
creator: Aditi Misra
creator: Andong Chen
creator: Edison Ong
creator: Robert Hampshire
creator: Yongqun "Oliver" He (YOH)
description: The Transportation System Ontology (TSO) is a community-based ontology developed to support open transportation and transportation-related knowledge and data representation, standardization and integration.
Format: OWL-DL
subject: TSO focuses on the area of transportation system.
creation date: 04-14-2020
version info: Vision Release: 0.0.26

BFO OWL specification label
type: AnnotationProperty
editor preferred label: BFO OWL specification label
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
editor preferred label: BFO CLIF specification label
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

has_MedDRA_id
type: AnnotationProperty

term mapping to NCIT ID
type: AnnotationProperty
textual definition: A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term
definition editor: Oliver He
sub property of: seeAlso

term mapping to UMLS CUI
type: AnnotationProperty
textual definition: A subproperty of seeAlso that represents a UMLS CUI identifier mapped to the specified term
definition editor: Oliver He
sub property of: seeAlso

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
textual definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

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

is direct form of
type: AnnotationProperty
textual definition: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
editor note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
textual definition: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is opposite of
type: AnnotationProperty
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: 'increase in temperature' is-opposite-of 'decrease in temperature'
textual definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
database_cross_reference: RO:0002604
has_obo_namespace: quality
id: is_opposite_of
is class level: true
is metadata tag: true
shorthand: is_opposite_of
label: is_opposite_of

is directional form of
type: AnnotationProperty
textual definition: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created by: cjm
creation date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

is homeomorphic for
type: AnnotationProperty
example of usage: part-of is homeomorphic for independent continuants.
textual definition: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
created by: cjm
creation date: 2018-10-21T19:46:34Z
comment: R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
sub property of: logical macro assertion on an object property

TRT cross-reference
type: AnnotationProperty
textual definition: A cross-referenced annotation from the Transportation Research Thesaurus (TRT)
definition editor: YOH
definition source: https://trt.trb.org/trt.asp

has_rank
type: AnnotationProperty
textual definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy

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_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in subset
type: AnnotationProperty
textual definition: Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
has exact synonym: Concept_In_Subset
label: in_subset

shorthand
type: AnnotationProperty

isDefinedBy
type: AnnotationProperty
OBO foundry unique label: is defined by

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: envo.owl
imported from: go.owl
imported from: iao.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
imported from: uberon.owl
temporal interpretation: axiom holds for all times
is homeomorphic for: continuant
is homeomorphic for: occurrent
is homeomorphic for: independent continuant
is homeomorphic for: realizable entity
is homeomorphic for: quality
is homeomorphic for: specifically dependent continuant
is homeomorphic for: generically dependent continuant
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: determined by
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: dron.owl
imported from: envo.owl
imported from: iao.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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
sub property of: topObjectProperty
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: dron.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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: envo.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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

obsolete preceded by
type: ObjectProperty
type: TransitiveProperty
imported from: OBO Relations Ontology
comment: accidentally included in BFO 1.2 proposal - should have been BFO_0000062
deprecated: true

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 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: OBO Relations Ontology
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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
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: OBO Relations Ontology
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred 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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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

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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

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
imported from: OPMI: Ontology of Precision Medicine and Investigation

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has_participant
sub property of: topObjectProperty
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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

is-aggregate-of
type: ObjectProperty
has obsolescence reason: BFO relation takes precedence.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
deprecated: true

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
sub property of: inheres in part of
sub property of: topObjectProperty
inverse of: bearer of
type: FunctionalProperty
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 at all times'
alternative term: inheres_in
imported from: dron.owl
imported from: envo.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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: bearer_of
alternative term: is bearer of
imported from: envo.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
temporal interpretation: axiom holds for all times
label: bearer_of
label: is bearer of

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: envo.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

has_participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
sub property of: topObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: inheres in
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: dron.owl
imported from: envo.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
label: 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
imported from: OPMI: Ontology of Precision Medicine and Investigation

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
sub property of: topObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
editor preferred label: concretizes
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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
textual definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

has role
type: ObjectProperty
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: OBO Relations Ontology

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

disposition of
type: ObjectProperty
sub property of: inheres in
textual definition: inverse of has disposition
imported from: OBO Relations Ontology
in subset: RO_0002259

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred 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: OBO Relations Ontology
temporal interpretation: axiom holds for all times
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in

has component activity
type: ObjectProperty
sub property of: has component process
imported from: OBO Relations Ontology
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
textual definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
imported from: OBO Relations Ontology
created by: dos
creation date: 2017-05-24T09:49:21Z

has effector activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulates (processual)
type: FunctionalProperty
textual definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
imported from: OBO Relations Ontology
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
definition editor: David Osumi-Sutherland
alternative term: <=
imported from: OBO Relations Ontology
in subset: ro-eco
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
imported from: OBO Relations Ontology
in subset: ro-eco
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
imported from: OBO Relations Ontology
in subset: ro-eco
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
definition editor: David Osumi-Sutherland
imported from: OBO Relations Ontology
in subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: di
imported from: OBO Relations Ontology
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

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: OBO Relations Ontology
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
definition editor: David Osumi-Sutherland
alternative term: starts_at_end_of
imported from: OBO Relations Ontology
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
definition editor: David Osumi-Sutherland
imported from: OBO Relations Ontology
in subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

starts before
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: starts during
property chain axiom: obsolete preceded by
definition editor: David Osumi-Sutherland
imported from: OBO Relations Ontology
in subset: ro-eco

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
definition editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
is direct form of: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
definition editor: David Osumi-Sutherland
alternative term: io
imported from: OBO Relations Ontology
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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
has curation status: pending final vetting
textual definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in subset: ro-eco

has component
type: ObjectProperty
sub property of: has part
has curation status: pending final vetting
textual definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
imported from: OBO Relations Ontology
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: determined by
inverse of: develops_into
type: TransitiveProperty
property chain axiom: part of
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
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: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
database_cross_reference: RO:0002203
has_obo_namespace: uberon
id: develops_into
shorthand: develops_into

regulates (processual)
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: ends with
property chain axiom: directly regulates
has curation status: pending final vetting
textual definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
definition editor: Chris Mungall
definition editor: David Hill
definition editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
OBO foundry unique label: regulates (processual)
elucidation: false
label: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates (processual)
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
textual definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
definition editor: Chris Mungall
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: negatively regulates (process to process)
is negative form of: regulates (processual)

positively regulates
type: ObjectProperty
sub property of: regulates (processual)
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
textual definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
definition editor: Chris Mungall
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: positively regulates (process to process)
is positive form of: regulates (processual)

has prototype
type: ObjectProperty
domain: Class
  union of: independent continuant
  union of: process
example of usage: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
has curation status: pending final vetting
textual definition: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
editor note: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
editor note: TODO: add homeomorphy axiom
editor note: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
definition editor: Chris Mungall
imported from: OBO Relations Ontology

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
has curation status: pending final vetting
textual definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
definition editor: Chris Mungall
alternative term: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
expand expression to: RO_0000053 some (RO_0000054 only ?Y)
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in
property chain axiom: capable of
property chain axiom: part of
has curation status: pending final vetting
textual definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
definition editor: Chris Mungall
alternative term: has function in
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
expand expression to: RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))

has active participant
type: ObjectProperty
sub property of: has_participant
example of usage: 'heart development' has active participant some Shh protein
has curation status: pending final vetting
textual definition: x has participant y if and only if x realizes some active role that inheres in y
editor note: This may be obsoleted and replaced by the original 'has agent' relation
definition editor: Chris Mungall
alternative term: has agent
imported from: envo.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: ro-eco

surrounded by
type: ObjectProperty
sub property of: adjacent_to
inverse of: surrounds
has curation status: pending final vetting
textual definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
textual definition: x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
definition editor: Chris Mungall
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
temporal interpretation: axiom holds for all times
database_cross_reference: RO:0002219
has_obo_namespace: uberon
id: surrounded_by
shorthand: surrounded_by
label: surrounded_by

adjacent_to
type: ObjectProperty
sub property of: spatially disjoint from
type: SymmetricProperty
domain: independent continuant
range: independent continuant
example of usage: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
has curation status: pending final vetting
textual definition: x adjacent to y if and only if x and y share a boundary.
textual definition: x adjacent_to y iff: x and y share a boundary
editor note: This relation acts as a join point with BSPO
definition editor: Chris Mungall
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
temporal interpretation: axiom holds for all times
database_cross_reference: RO:0002220
has_obo_namespace: uberon
id: adjacent_to
shorthand: adjacent_to
label: adjacent to

surrounds
type: ObjectProperty
sub property of: adjacent_to
has curation status: pending final vetting
textual definition: inverse of surrounded by
textual definition: inverse of surrounded_by
definition editor: Chris Mungall
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
temporal interpretation: axiom holds for all times
database_cross_reference: RO:0002221
has_obo_namespace: uberon
id: surrounds
in subset: RO_0002259
shorthand: surrounds

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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
has curation status: pending final vetting
textual definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
imported from: OBO Relations Ontology
in subset: ro-eco

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: pending final vetting
textual definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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.
definition editor: Chris Mungall
alternative term: started by
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
imported from: uberon.owl
database_cross_reference: RO:0002224
has_obo_namespace: uberon
id: starts_with
in subset: ro-eco
shorthand: starts_with

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
has curation status: pending final vetting
textual definition: inverse of ends with
definition editor: Chris Mungall
imported from: OBO Relations Ontology
in subset: ro-eco

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
has curation status: pending final vetting
textual definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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.
definition editor: Chris Mungall
alternative term: finished by
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
imported from: uberon.owl
database_cross_reference: RO:0002230
has_obo_namespace: uberon
id: ends_with
in subset: ro-eco
shorthand: ends_with

has input
type: ObjectProperty
sub property of: has_participant
inverse of: input of
domain: process
range: material entity
property chain axiom: starts with
has curation status: pending final vetting
textual definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
textual definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: consumes
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
in subset: ro-eco

has output
type: ObjectProperty
sub property of: has_participant
inverse of: output of
property chain axiom: ends with
has curation status: pending final vetting
textual definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
definition editor: Chris Mungall
alternative term: produces
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
in subset: ro-eco

has developmental contribution from
type: ObjectProperty
sub property of: determined by
type: TransitiveProperty
property chain axiom: has part
property chain axiom: develops_from
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
database_cross_reference: RO:0002254
has_obo_namespace: uberon
id: has_developmental_contribution_from
shorthand: has_developmental_contribution_from

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
imported from: OBO Relations Ontology
is positive form of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
imported from: OBO Relations Ontology
is negative form of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

inheres in part of
type: ObjectProperty
sub property of: depends on
property chain axiom: inheres in
property chain axiom: part of
textual definition: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
temporal interpretation: axiom holds for all times

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: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
temporal interpretation: axiom holds for all times

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition editor: Chris Mungall
alternative term: catalyzes
alternative term: executes
alternative term: has
alternative term: is catalyzing
alternative term: is executing
curator note: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
curator note: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

functionally related to
type: ObjectProperty
textual definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
definition editor: Chris Mungall
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

enabled by
type: ObjectProperty
sub property of: functionally related to
sub property of:
  inverse of: capable of
textual definition: inverse of enables
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
textual definition: inverse of regulates
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
OBO foundry unique label: regulated by (processual)
in subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
textual definition: inverse of negatively regulates
definition editor: Chris Mungall
imported from: OBO Relations Ontology
in subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
textual definition: inverse of positively regulates
definition editor: Chris Mungall
imported from: OBO Relations Ontology
in subset: RO_0002259

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
textual definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
temporal interpretation: axiom holds for all times

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
textual definition: has member is a mereological relation between a collection and an item.
definition source: SIO
imported from: OAE: Ontology of Adverse Events
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
imported from: uberon.owl
temporal interpretation: axiom holds for all times
database_cross_reference: RO:0002351
has_obo_namespace: uberon
id: has_member
shorthand: has_member

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
textual definition: inverse of has input
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
in subset: RO_0002259
in subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
textual definition: inverse of has output
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
in subset: RO_0002259
in subset: ro-eco

formed as result of
type: ObjectProperty
sub property of: output of
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

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: OPMI: Ontology of Precision Medicine and Investigation
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 direct input
type: ObjectProperty
sub property of: has input
property chain axiom: starts with
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
has curation status: requires discussion
textual definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: directly consumes
curator note: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
imported from: OBO Relations Ontology

obsolete has direct output
type: ObjectProperty
example of usage: translation SubClassOf has_direct_output some protein
has curation status: requires discussion
textual definition: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
definition editor: Chris Mungall
alternative term: directly produces
imported from: OBO Relations Ontology
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
has curation status: requires discussion
textual definition: inverse of upstream of
definition editor: Chris Mungall
imported from: OBO Relations Ontology

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
definition editor: Chris Mungall
imported from: OBO Relations Ontology

directly activates
type: ObjectProperty
sub property of: directly positively regulates
has curation status: requires discussion
textual definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: directly positively regulates
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: directly activates (process to process)

indirectly activates
type: ObjectProperty
sub property of: positively regulates
type: TransitiveProperty
property chain axiom: directly activates
property chain axiom: indirectly inhibits
textual definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: indirectly positively regulates
imported from: OBO Relations Ontology
is indirect form of: positively regulates

directly inhibits
type: ObjectProperty
sub property of: directly negatively regulates
definition editor: Chris Mungall
alternative term: directly negatively regulates
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: directly inhibits (process to process)

indirectly inhibits
type: ObjectProperty
sub property of: negatively regulates
type: TransitiveProperty
property chain axiom: directly inhibits
has curation status: requires discussion
definition editor: Chris Mungall
alternative term: indirectly negatively regulates
imported from: OBO Relations Ontology
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
sub property of: related via dependence to
has curation status: requires discussion
textual definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
has curation status: requires discussion
textual definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
has curation status: requires discussion
textual definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: obsolete has direct output
property chain axiom: has direct input
has curation status: requires discussion
textual definition: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
editor note: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
definition editor: Chris Mungall
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
domain: process
range: process
has curation status: requires discussion
textual definition: transitive form of directly_provides_input_for
definition editor: Chris Mungall
curator note: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
imported from: OBO Relations Ontology
OBO foundry unique label: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
textual definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
definition editor: Chris Mungall
alternative term: influences (processual)
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
textual definition: inverse of causally upstream of or within
definition editor: Chris Mungall
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
in subset: RO_0002259

composed primarily of
type: ObjectProperty
sub property of: has part
example of usage: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
textual definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
textual definition: x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
temporal interpretation: axiom holds for all times
has_alternative_id: UBREL:0000002
database_cross_reference: RO:0002473
has_obo_namespace: uberon
id: composed_primarily_of
in subset: ro-eco
shorthand: composed_primarily_of

causal agent in
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: has causal agent
textual definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
textual definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

depends on
type: ObjectProperty
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

causal relation between material entities
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: material entity
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

determined by
type: ObjectProperty
sub property of: part of
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
type: TransitiveProperty
domain: system
range: material entity
property chain axiom: has part
property chain axiom: develops_from
example of usage: A coral reef environment is determined by a particular coral reef
textual definition: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
editor note: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/24330602
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
OBO foundry unique label: determined by (system to material entity)
creator: Chris Mungall
creator: Pier Buttigieg
database_cross_reference: RO:0002507
has_obo_namespace: uberon
id: has_material_contribution_from
in subset: ro-eco
shorthand: has_material_contribution_from
label: has material contribution from

determines
type: ObjectProperty
sub property of: causally influences
textual definition: inverse of determined by
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
OBO foundry unique label: determines (material entity to system)
in subset: RO_0002259
in subset: ro-eco

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between material entities
domain: system
range: material entity
property chain axiom: determined by
property chain axiom: part of
textual definition: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
definition editor: Chris Mungall
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: ro-eco

causally influenced by
type: ObjectProperty
sub property of: causal relation between material entities
inverse of: causally influences
definition editor: Chris Mungall
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
OBO foundry unique label: causally influenced by (material entity to material entity)

causally influences
type: ObjectProperty
sub property of: causal relation between material entities
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
textual definition: Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
definition editor: Chris Mungall
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
OBO foundry unique label: causally influences (material entity to material entity)

directly regulates
type: ObjectProperty
sub property of: regulates (processual)
sub property of: immediately causally upstream of
textual definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
definition editor: Chris Mungall
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
OBO foundry unique label: directly regulates (processual)
is direct form of: regulates (processual)

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
textual definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
definition editor: Chris Mungall
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

has causal agent
type: ObjectProperty
sub property of: causally related to
textual definition: Inverse of 'causal agent in'
definition source: causal-relations
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

related via dependence to
type: ObjectProperty
textual definition: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
textual definition: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: directly positively regulates (process to process)
is positive form of: directly regulates

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
textual definition: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
definition source: causal-relations
imported from: OBO Relations Ontology
OBO foundry unique label: directly negatively regulates (process to process)
is negative form of: directly regulates

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: OBO Relations Ontology
is negative form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: OBO Relations Ontology
is positive form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
textual definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
editor note: TODO: Add homeomorphy axiom
imported from: OBO Relations Ontology
is homeomorphic for: continuant
is homeomorphic for: occurrent
creator: bgee.unil.ch
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000041
database_cross_reference: SO:similar_to
has exact synonym: sameness
has exact synonym: similar to
has_related_synonym: correspondence
has_related_synonym: resemblance

has start time
type: ObjectProperty

has characteristics
type: ObjectProperty

has start location
type: ObjectProperty

has end location
type: ObjectProperty

has end time
type: ObjectProperty

uses vehicle
type: ObjectProperty

has passenger
type: ObjectProperty

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
editor preferred 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: ico.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
subclass of: Restriction
  on property: part of
  all values from: continuant
subclass of: Restriction
  on property: has prototype
  all values from: continuant
subclass of: Restriction
  on property: in similarity relationship with
  all values from: continuant
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: OBO Relations Ontology
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
subclass of: Restriction
  on property: part of
  all values from: occurrent
subclass of: Restriction
  on property: in similarity relationship with
  all values from: occurrent
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor preferred 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: dron.owl
imported from: envo.owl
imported from: iao.owl
imported from: ico.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: OBO Relations Ontology
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
subclass of: Restriction
  on property: part of
  all values from: independent 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: 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: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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]

spatial region
type: Class
subclass of: immaterial entity
imported from: OBO Relations Ontology

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
imported from: OPMI: Ontology of Precision Medicine and Investigation
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
subclass of: Restriction
  on property: has prototype
  all values from: process
BFO OWL specification label: process
BFO CLIF specification label: Process
editor preferred 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: ico.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: OBO Relations Ontology
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
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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
subclass of: Restriction
  on property: part of
  all values from: realizable entity
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: dron.owl
imported from: envo.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
imported from: OBO Relations Ontology
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
subclass of: Restriction
  on property: part of
  all values from: quality
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: bfo.owl
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
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: bfo.owl
imported from: dron.owl
imported from: envo.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: OBO Relations Ontology
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: dron.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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]

fiat object
type: Class
subclass of: material entity
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
label: fiat object part

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

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: envo.owl
imported from: iao.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
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: dron.owl
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
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
subclass of: Restriction
  on property: part of
  all values from: generically dependent 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: envo.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
imported from: OBO Relations Ontology
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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
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
imported from: OPMI: Ontology of Precision Medicine and Investigation
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: bfo.owl
imported from: dron.owl
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology
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: envo.owl
imported from: iao.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: OBO Relations Ontology

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
imported from: OPMI: Ontology of Precision Medicine and Investigation
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]

organism or virus or viroid
type: Class
subclass of: organismal entity
textual definition: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

geographic feature
type: Class
subclass of: astronomical body part
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
database_cross_reference: https://en.wikipedia.org/wiki/Geographic_feature
has exact synonym: macroscopic spatial feature
in subset: envoPolar
comment: May appear on a map.

anthropogenic geographic feature
type: Class
equivalent class: Class
  intersection of: astronomical body part
  intersection of: Restriction
    on property: formed as result of
    some values from: anthropisation
subclass of: geographic feature
subclass of: Restriction
  on property: formed as result of
  some values from: anthropisation
textual definition: An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
database_cross_reference: FTT:78
database_cross_reference: TGN:50001
has_related_synonym: man-made feature
has_related_synonym: manmade feature

populated place
type: Class
subclass of: environmental zone
textual definition: Place or area with clustered or scattered buildings and a permanent human population.
imported from: envo.owl
has_broad_synonym: place
database_cross_reference: FTT:1097
database_cross_reference: FTT:33
database_cross_reference: Geonames:P.PPL
database_cross_reference: Geonames:P.PPLS
database_cross_reference: TGN:22201
database_cross_reference: TGN:83002
database_cross_reference: https://en.wikipedia.org/wiki/Populated_place
has exact synonym: inhabited place
has exact synonym: populated place
has exact synonym: populated places
has exact synonym: settlement
has_obo_namespace: ENVO
has_related_synonym: inhabited region
has_related_synonym: populated locality
id: ENVO:00000062

construction
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: output of
    some values from: construction process
equivalent class: Class
  intersection of: environmental feature
  intersection of: Restriction
    on property: output of
    some values from: construction process
subclass of: anthropogenic geographic feature
subclass of: Restriction
  on property: part of
  some values from: technosphere
subclass of: Restriction
  on property: output of
  some values from: construction process
textual definition: A feature that has been constructed by deliberate human effort.
editor note: "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: constructed feature

building
type: Class
subclass of: construction
subclass of: Restriction
  on property: has part
  some values from: building part
textual definition: A permanent walled and roofed construction.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
database_cross_reference: FTT:42
database_cross_reference: Geonames:S.BLDG
database_cross_reference: LTER:76
database_cross_reference: TGN:51011
database_cross_reference: https://en.wikipedia.org/wiki/Building
has exact synonym: BUILDING
has exact synonym: building

city
type: Class
subclass of: dense settlement
textual definition: Incorporated populated place.
imported from: envo.owl
has_broad_synonym: urban area
database_cross_reference: EcoLexicon:city
database_cross_reference: FTT:430
database_cross_reference: FTT:483
database_cross_reference: FTT:484
database_cross_reference: FTT:485
database_cross_reference: SWEETRealm:City
database_cross_reference: TGN:83020
database_cross_reference: TGN:83040
database_cross_reference: TGN:83043
database_cross_reference: https://en.wikipedia.org/wiki/City
has_obo_namespace: ENVO
id: ENVO:00000856

mesoscopic physical object
type: Class
subclass of: object
subclass of: environmental feature
textual definition: An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
textual definition: An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance.
alternative term: mesoscopic physical object
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter.
label: physical object of mesoscopic geological size

environmental feature
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: determines
    some values from: environmental system
subclass of: material entity
subclass of: Restriction
  on property: determines
  some values from: environmental system
textual definition: A material entity which determines an environmental system.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_obo_namespace: ENVO
id: ENVO:00002297
comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.

manufactured product
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: output of
    some values from: manufacturing process
subclass of: anthropogenic abiotic mesoscopic feature
subclass of: Restriction
  on property: output of
  some values from: manufacturing process
textual definition: A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: manufactured good

anthropogenic abiotic mesoscopic feature
type: Class
subclass of: abiotic mesoscopic physical object
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_obo_namespace: ENVO
id: ENVO:00003075

environmental material
type: Class
subclass of: fiat object
subclass of: material entity
textual definition: A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
textual definition: A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: portion of environmental material
comment: Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.

abiotic mesoscopic physical object
type: Class
subclass of: mesoscopic physical object
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_obo_namespace: ENVO
id: ENVO:01000010

environmental system
type: Class
subclass of: system
textual definition: A system which has the disposition to environ one or more material entities.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
creation date: 2013-09-23T16:04:08Z
database_cross_reference: EcoLexicon:environment
has exact synonym: environment
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.

anthropogenic environment
type: Class
equivalent class: Class
  intersection of: environmental system
  intersection of: Restriction
    on property: determined by
    some values from: Restriction
      on property: output of
      some values from: anthropisation
subclass of: environmental system
subclass of: Restriction
  on property: determined by
  some values from: Restriction
    on property: output of
    some values from: anthropisation
textual definition: An anthropogenic environment is an environmental system which is the product of human activity.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.

environmental zone
type: Class
subclass of: site
textual definition: A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
imported from: envo.owl
has_related_synonym: environmental area
in subset: envoPolar
comment: Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.

building part
type: Class
subclass of: construction
subclass of: Restriction
  on property: part of
  some values from: building
textual definition: A building part is a construction which is part of a building.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.

outer space
type: Class
subclass of: environmental feature
subclass of: environmental material
textual definition: Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_broad_synonym: space
in subset: envoAstro

dense settlement
type: Class
subclass of: populated place
textual definition: A settlement with a high density of buildings and inhabitants.
editor note: See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx
imported from: envo.owl
comment: The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.

human dwelling
type: Class
subclass of: construction
subclass of: domestic building
textual definition: A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
editor note: See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
editor note: Subclasses will be added by inference.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

rural area
type: Class
subclass of: anthropised terrestrial environmental zone
textual definition: An area which is outside of a town, city, or urban area. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements.
imported from: envo.owl
comment: A class created fro SDGIO. The definition of rural is highly varied, dealing with areas, settlements, and populations interchangeably. The 'rural' classes in ENVO aim to clarify these differing definitions. See issue #272.

astronomical body
type: Class
subclass of: astronomical object
textual definition: An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_related_synonym: celestial body
in subset: envoAstro
comment: Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.

astronomical object
type: Class
subclass of: object
subclass of: environmental feature
subclass of: Restriction
  on property: has quality
  some values from: geodiversity
subclass of: Restriction
  on property: surrounded by
  some values from: outer space
subclass of: Restriction
  on property: has part
  min qualified cardinality: 1
  on class: astronomical body
textual definition: An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_related_synonym: celestial object
in subset: envoAstro
comment: If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.

astronomical body part
type: Class
subclass of: fiat object
subclass of: environmental feature
subclass of: Restriction
  on property: part of
  some values from: astronomical body
textual definition: A material part of an astronomical body.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: envoAstro
in subset: envoPolar

biosphere
type: Class
subclass of: astronomical body part
subclass of: ecosystem
subclass of: Restriction
  on property: has part
  some values from: collection of organisms
textual definition: A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
textual definition: A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with.
editor note: Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: envoAstro
in subset: envoPolar
comment: The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.

natural environment
type: Class
equivalent class: Class
  intersection of: environmental system
  intersection of: Class
    complement of: Restriction
      on property: contains process
      some values from: anthropisation
  intersection of: Class
    complement of: Restriction
      on property: formed as result of
      some values from: anthropisation
equivalent class: Class
  intersection of: environmental system
  intersection of: Class
    complement of: Restriction
      on property: formed as result of
      some values from: anthropisation
subclass of: environmental system
textual definition: An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
alternative term: non-anthropised environment
alternative term: non-anthropized environment
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.

anthropisation
type: Class
equivalent class: Class
  intersection of: anthropogenic ecosystem conversion process
  intersection of: Restriction
    on property: has input
    some values from: natural environment
  intersection of: Restriction
    on property: has output
    some values from: anthropogenic environment
equivalent class: Class
  intersection of: anthropogenic environmental process
  intersection of: Restriction
    on property: has input
    some values from: natural environment
  intersection of: Restriction
    on property: has output
    some values from: anthropogenic environment
subclass of: anthropogenic ecosystem conversion process
subclass of: anthropogenic environmental process
subclass of: Restriction
  on property: has input
  some values from: natural environment
subclass of: Restriction
  on property: has output
  some values from: anthropogenic environment
textual definition: A process during which a natural environmental system is altered by human action.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: anthropization
comment: An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.

technosphere
type: Class
subclass of: astronomical body part
subclass of: Restriction
  on property: has part
  some values from: construction
subclass of: Restriction
  on property: has part
  some values from: manufactured product
subclass of: Restriction
  on property: overlaps
  some values from: biosphere
textual definition: A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body.
textual definition: An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: envoAstro
comment: The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.

manufacturing process
type: Class
equivalent class: Class
  intersection of: anthropisation
  intersection of: Restriction
    on property: has output
    some values from: manufactured product
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has output
    some values from: manufactured product
subclass of: anthropisation
subclass of: planned process
subclass of: Restriction
  on property: has output
  some values from: manufactured product
textual definition: A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.

construction process
type: Class
equivalent class: Class
  intersection of: anthropisation
  intersection of: Restriction
    on property: has output
    some values from: construction
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has output
    some values from: construction
subclass of: anthropisation
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: material transport process
subclass of: Restriction
  on property: has part
  some values from: material transformation process
subclass of: Restriction
  on property: has output
  some values from: construction
textual definition: An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
editor note: The nature of "structures" must be further specified.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

ecosystem
type: Class
equivalent class: Class
  union of: Class
    intersection of: environmental system
    intersection of: Restriction
      on property: has part
      some values from: cellular organisms
  union of: Restriction
    on property: has part
    some values from: collection of organisms
  union of: Restriction
    on property: determined by
    some values from: cellular organisms
  union of: Restriction
    on property: determined by
    some values from: collection of organisms
  union of: Restriction
    on property: determined by
    some values from: plant anatomical entity
  union of: Restriction
    on property: determined by
    some values from: anatomical entity
subclass of: environmental system
textual definition: An environmental system which includes both living and non-living components.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_alternative_id: LTER:173
comment: This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.

geodiversity
type: Class
subclass of: physical object quality
textual definition: A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.

active ecosystem management process
type: Class
subclass of: anthropogenic modulatory intervention process
subclass of: anthropogenic environmental process
subclass of: Restriction
  on property: has_participant
  some values from: ecosystem
textual definition: A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: ecosystem management
has_related_synonym: Umweltmaßnahme @de
has_related_synonym: environmental management

terrestrial environmental zone
type: Class
subclass of: environmental zone
textual definition: An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
imported from: envo.owl

anthropised terrestrial environmental zone
type: Class
subclass of: terrestrial environmental zone
textual definition: A terrestrial zone which is bounded by constructed, manufactured, or other anthropogenic material entities.
imported from: envo.owl

anthropogenic ecosystem conversion process
type: Class
subclass of: anthropogenic environmental process
textual definition: A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
created by: http://orcid.org/0000-0002-4366-3088

planned environmental usage process
type: Class
subclass of: anthropogenic environmental process
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: active ecosystem management process
subclass of: Restriction
  on property: has_participant
  some values from: Class
    union of: anthropogenic environment
    union of: natural environment
textual definition: A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
created by: http://orcid.org/0000-0002-4366-3088

usage of an environment for residential activity
type: Class
subclass of: planned environmental usage process
subclass of: Restriction
  on property: has_participant
  some values from: human dwelling
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: ecological community
    intersection of: Restriction
      on property: composed primarily of
      some values from: Homo sapiens
textual definition: A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
created by: http://orcid.org/0000-0002-4366-3088
has_broad_synonym: residential
comment: This class does not include environments which are primarily used for commerce or industry.

domestic building
type: Class
equivalent class: Class
  intersection of: building
  intersection of: Restriction
    on property: participates in
    some values from: usage of an environment for residential activity
subclass of: building
subclass of: Restriction
  on property: participates in
  some values from: usage of an environment for residential activity
textual definition: A building which is primarily used for the long-term habitation of humans.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
created by: http://orcid.org/0000-0002-4366-3088
creation date: 2018-10-04T14:04:49Z

transportation
type: Class
subclass of: material transport process
textual definition: A planned process that is the movement of people, animals and goods from one location to another.
imported from: envo.owl
creator: cjm

environmental system process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      union of: environmental feature
      union of: environmental material
      union of: environmental system
subclass of: process
subclass of: Restriction
  on property: has_participant
  some values from: Class
    union of: environmental feature
    union of: environmental material
    union of: environmental system
textual definition: A process in which includes the components of an environmental system as participants.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: This is a convenience class for organisation and should not be used for annotation.

anthropogenic modulatory intervention process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: regulates (processual)
    some values from: environmental system process
  intersection of: Restriction
    on property: has active participant
    some values from: Homo sapiens
subclass of: planned process
subclass of: Restriction
  on property: regulates (processual)
  some values from: environmental system process
subclass of: Restriction
  on property: has active participant
  some values from: Homo sapiens
textual definition: A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Relabel the obo foundry unique label to be generic process

anthropogenic environmental process
type: Class
equivalent class: Class
  intersection of: environmental system process
  intersection of: Restriction
    on property: has active participant
    some values from: Homo sapiens
subclass of: environmental system process
subclass of: Restriction
  on property: has active participant
  some values from: Homo sapiens
textual definition: An environmental process which is driven by the action of humans.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

material transport process
type: Class
subclass of: environmental system process
subclass of: Restriction
  on property: has output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has quality
      some values from: displaced
textual definition: A process during which material is displaced from its original location and transported either to a new location or back to the original location.
definition editor: http://orcid.org/0000-0002-3410-4655
definition editor: http://orcid.org/0000-0002-4366-3088
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: envoPolar
comment: Experimental class for structural purposes not recommended for annotation.

material transformation process
type: Class
subclass of: environmental system process
subclass of: Restriction
  on property: has input
  some values from: environmental material
subclass of: Restriction
  on property: has output
  some values from: environmental material
textual definition: A process during which a portion of some environmental material is converted into a different material or a collection of materials.
editor note: A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
definition editor: http://orcid.org/0000-0002-3410-4655
definition editor: http://orcid.org/0000-0002-4366-3088
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: envoPolar
comment: Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.

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
imported from: OPMI: Ontology of Precision Medicine and Investigation

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
imported from: OPMI: Ontology of Precision Medicine and Investigation

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

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: envo.owl
imported from: iao.owl
imported from: ico.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
imported from: OPMI: Ontology of Precision Medicine and Investigation

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: metadata complete
textual definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
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: envo.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 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: envo.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
imported from: OPMI: Ontology of Precision Medicine and Investigation
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

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: iao.owl
imported from: ico.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

social act
type: Class
subclass of: process
subclass of: planned process
example of usage: Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
textual definition: A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that needs to be perceived.
textual definition: A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
definition editor: Mathias Brochhausen
imported from: ico.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.

socio-legal generically dependent continuant
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: declaration
subclass of: generically dependent continuant
example of usage: the claim of a piece of land, the obligation to pay rent to the owner of a rental property
textual definition: Socio-legal generically dependent continuants are generically dependent continuants that come into existence through declarations and are concretized as roles. They differ from information content entities in that they are not about something, but exist as quasi-abstract social entities. Socio-legal generically dependent continuants are not concretized as qualities inhering in independent continuants, but only as realizable entities borne by an organism or an aggregate of organisms.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

declaration
type: Class
equivalent class: Class
  intersection of: Class
    union of: Restriction
      on property: IAO_0021011
      some values from: Class
        union of: role
        union of: socio-legal generically dependent continuant
    union of: Restriction
      on property: IAO_0021012
      some values from: socio-legal generically dependent continuant
    union of: Restriction
      on property: has_specified_output
      some values from: Class
        union of: role
        union of: socio-legal generically dependent continuant
  intersection of: Restriction
    on property: realizes
    some values from: declaration performer role
  intersection of: Restriction
    on property: has active participant
    some values from: Class
      intersection of: Class
        union of: Homo sapiens
        union of: organization
        union of: collection of humans
        union of: aggregate of organizations
      intersection of: Restriction
        on property: bearer of
        some values from: declaration performer role
subclass of: social act
example of usage: my consenting verbally to buy a used TV set for $ 500, Jane Doe's signing of the divorce papers, John Robie's taking of Mrs. Steven's jewels
textual definition: A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or revokes a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

declaration performer role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
      union of: collection of humans
      union of: aggregate of organizations
  intersection of: Restriction
    on property: realized in
    all values from: declaration
example of usage: a judge's role of signing a court order, a hospital committee's to sanction conformance to a specific guideline for hospital employees.
textual definition: A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

root
type: Class
subclass of: material entity
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: all
id: NCBITaxon:1

Viruses
type: Class
subclass of: root
subclass of: organism
editor preferred label: Viruses
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_related_synonym: Vira
has_related_synonym: Viridae
has_related_synonym: viruses

Teleostomi
type: Class
subclass of: Gnathostomata <vertebrate>
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Euteleostomi
type: Class
subclass of: Teleostomi
subclass of: Vertebrata <Metazoa>
subclass of: Gnathostomata <vertebrate>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: bony vertebrates

cellular organisms
type: Class
subclass of: root
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: biota
id: NCBITaxon:131567

Dipnotetrapodomorpha
type: Class
subclass of: Euteleostomi
subclass of: Sarcopterygii
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Boreoeutheria
type: Class
subclass of: Eutheria
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_related_synonym: Boreotheria

Bacteria
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: eubacteria
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
has_related_synonym: not Bacteria Haeckel 1894
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Homininae
type: Class
subclass of: Hominidae
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_related_synonym: Homo/Pan/Gorilla group

Archaea
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred label: Archaea
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
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

Eukaryota
type: Class
subclass of: cellular organisms
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_rank: NCBITaxon superkingdom
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
id: NCBITaxon:2759

Euarchontoglires
type: Class
subclass of: Boreoeutheria
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Simiiformes
type: Class
subclass of: Euarchontoglires
subclass of: Haplorrhini
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_related_synonym: Anthropoidea

Hominoidea
type: Class
subclass of: Catarrhini
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: ape
has exact synonym: apes

Tetrapoda
type: Class
subclass of: Euteleostomi
subclass of: Dipnotetrapodomorpha
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: tetrapods

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: amniotes

Theria <Mammalia>
type: Class
subclass of: Mammalia
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: Theria

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Fungi/Metazoa group
has_related_synonym: opisthokonts
id: NCBITaxon:33154

Metazoa
type: Class
subclass of: Opisthokonta
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: metazoans
has exact synonym: multicellular animals
has_related_synonym: Animalia
has_related_synonym: animals

Bilateria
type: Class
subclass of: Opisthokonta
subclass of: Eumetazoa
editor preferred label: Bilateria
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Deuterostomia
type: Class
subclass of: Bilateria
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: deuterostomes

Haplorrhini
type: Class
subclass of: Primates
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: mammals
has_related_synonym: mammals

Eumetazoa
type: Class
subclass of: Metazoa
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Chordata
type: Class
subclass of: Deuterostomia
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: chordates
has_related_synonym: chordates

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
subclass of: Chordata
subclass of: Craniata <chordata>
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: Vertebrata
has exact synonym: vertebrates
has_related_synonym: vertebrates

Gnathostomata <vertebrate>
type: Class
subclass of: Vertebrata <Metazoa>
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: Gnathostomata
has exact synonym: jawed vertebrates

Sarcopterygii
type: Class
subclass of: Euteleostomi
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Craniata <chordata>
type: Class
subclass of: Chordata
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: Craniata

Eutheria
type: Class
subclass of: Theria <Mammalia>
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: eutherian mammals
has exact synonym: placental mammals
has exact synonym: placentals
has_related_synonym: Placentalia
has_related_synonym: placentals

Primates
type: Class
subclass of: Euarchontoglires
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: primate
has_related_synonym: Primata
has_related_synonym: primates

Catarrhini
type: Class
subclass of: Simiiformes
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

Hominidae
type: Class
subclass of: Hominoidea
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: great apes
has_related_synonym: Pongidae

Homo
type: Class
subclass of: Homininae
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: humans

Homo sapiens
type: Class
subclass of: Eukaryota
subclass of: Euarchontoglires
subclass of: Catarrhini
subclass of: Homo
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
alternative term: person
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
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: humans

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
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

surgery
type: Class
subclass of: medical procedure
textual definition: Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery.
definition editor: YH, SS
alternative term: surgical procedure
definition source: WEB: http://en.wikipedia.org/wiki/Surgery
definition source: WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
imported from: OAE: Ontology of Adverse Events
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
has_MedDRA_id: 10042609

medical procedure
type: Class
subclass of: medical intervention
textual definition: a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
definition editor: YH, SS
definition source: WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
imported from: OAE: Ontology of Adverse Events
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

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: dron.owl
imported from: envo.owl
imported from: ico.owl
imported from: OAE: Ontology of Adverse Events
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: vo.owl

population
type: Class
subclass of: material entity
editor preferred label: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: pending final vetting
textual definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
definition editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process
imported from: obi.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

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 organization is a continuant entity which can play 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: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: object
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: organizational term
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: dron.owl
imported from: envo.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

health care encounter
type: Class
subclass of: process
textual definition: A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

injury
type: Class
subclass of: material entity
textual definition: A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure.
editor note: At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5
curator note: creation date: 2011-09-20T09:57:44Z
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: http://purl.obolibrary.org/obo/ogms.owl

human social role
type: Class
subclass of: organism social role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
textual definition: A social role inhering in a human being.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

party to a legal entity
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      union of: Homo sapiens
      union of: organization
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

party to a legal proceeding
type: Class
subclass of: party to a legal entity
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

party to a legal agreement
type: Class
subclass of: party to a legal entity
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

party to a marriage contract
type: Class
subclass of: party to a legal agreement
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

party to a power of attorney
type: Class
subclass of: party to a legal entity
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

gender role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: organism
textual definition: A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Gender_role
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

male gender role
type: Class
subclass of: gender role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: inheres in
    all values from: organism
textual definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
definition editor: Mathias Brochhausen
alternative term: male gender
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

female gender role
type: Class
subclass of: gender role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: inheres in
    all values from: organism
textual definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
definition editor: Mathias Brochhausen
alternative term: female gender
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

human health care role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: health care encounter
textual definition: A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
definition editor: William R. Hogan
alternative term: health care role
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Mathias Brochhausen

patient role
type: Class
subclass of: human health care role
subclass of: Restriction
  on property: inheres in
  some values from: organism
textual definition: A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
definition editor: Amanda Hicks
definition editor: Mathias Brochhausen
alternative term: patient
definition source: CAFE domain expert working group.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.

health care provider role
type: Class
subclass of: human health care role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      union of: Homo sapiens
      union of: organization
textual definition: A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: William R. Hogan

physician role
type: Class
subclass of: health care provider role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
textual definition: A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
definition editor: Mathias Brochhausen
alternative term: physician
definition source: http://en.wikipedia.org/wiki/Physician
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

nurse role
type: Class
subclass of: health care provider role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
textual definition: A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
definition editor: Mathias Brochhausen
alternative term: nurse
definition source: based on: http://en.wikipedia.org/wiki/Nursing
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

health care provider organization role
type: Class
subclass of: organization health care role
subclass of: Restriction
  on property: realized in
  some values from: health care encounter
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division).

person health care provider role
type: Class
subclass of: human social role
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

physician practice
type: Class
subclass of: health care provider organization role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organization
    intersection of: Restriction
      on property: has organization member
      min qualified cardinality: 2
      on class: Restriction
        on property: bearer of
        some values from: physician role
textual definition: A health care provider organization role that inheres in an organization consisting of two or more physicians.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

integrated delivery network
type: Class
subclass of: health care provider organization role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organization
    intersection of: Restriction
      on property: has organization member
      all values from: organization
textual definition: A health care provider organization role that inheres in an organization that is comprised of other organizations.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

collection of organisms
type: Class
subclass of: material entity
textual definition: An object aggregate of organisms.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class.

collection of humans
type: Class
subclass of: collection of organisms
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: An object aggregate all of whose components are human beings.

role in human social processes
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: organization
    union of: organism
subclass of: Restriction
  on property: inheres in
  all values from: Class
    union of: organization
    union of: organism
textual definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Previous definition: A role played by an entity in human social processes.

organization social role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: inheres in
  some values from: organization
textual definition: A role in human social processes that inheres in an organization.
definition editor: William R. Hogan
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.

organism social role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: inheres in
  some values from: organism
textual definition: A role in human social processes that inheres in an organism.
definition editor: William R. Hogan Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
comment: Previous definition: A role in human social processes played by an organism.

organization health care role
type: Class
subclass of: organization social role
textual definition: An organization social role that is realized by a health care process.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Previous definition: An organization social role played by an organization in health care processes.

human patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: inheres in
    some values from: Homo sapiens
textual definition: A patient role that inheres in a human being.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

aggregate of organizations
type: Class
equivalent class: Class
  intersection of: Class
    complement of: organization
  intersection of: Restriction
    on property: is-aggregate-of
    all values from: organization
  intersection of: Restriction
    on property: is-aggregate-of
    min qualified cardinality: 2
    on class: organization
subclass of: material entity
textual definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
definition editor: William R. Hogan Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

legal person role
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      union of: Homo sapiens
      union of: collection of humans
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      union of: Homo sapiens
      union of: collection of humans
textual definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
definition editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.

hospital role
type: Class
subclass of: health care provider organization role
textual definition: A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

school role
type: Class
subclass of: organization social role
definition editor: An organization social role that inheres in an organization and is realized by providing formal education to students.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

school organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: bearer of
    some values from: school role
subclass of: organization
textual definition: An organization that is the bearer of a school role.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

student role
type: Class
subclass of: human role within an organization
subclass of: Restriction
  on property: concretizes
  some values from: Class
    intersection of: socio-legal generically dependent continuant
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: declaration
        intersection of: Restriction
textual definition: A human social role that is realized by the process of formal education that the bearer undergoes.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

nursery school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

primary school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

secondary school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

pediatric trauma patient role
type: Class
subclass of: human patient role
textual definition: A trauma patient role that inheres in a homo sapiens who is under the age of 15 years.
definition editor: Amanda Hicks
alternative term: pediatric trauma patient
definition source: The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years."
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

injured patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: has part
        some values from: injury
subclass of: patient role
textual definition: A patient role that inheres an organism suffering one or more injuries.
definition editor: Amanda Hicks
alternative term: injured patient
definition source: The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

burn patient role
type: Class
subclass of: injured patient role
textual definition: A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn.
definition editor: Amanda Hicks
definition editor: The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn.
definition editor: burn patient
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

physiatrist role
type: Class
subclass of: physician role
textual definition: A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient.
definition editor: Amanda Hicks
alternative term: physiatrist
definition source: The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.

trauma patient role
type: Class
subclass of: patient role
textual definition: A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury.
definition editor: Amanda Hicks
alternative term: trauma patient
definition source: The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

residence function
type: Class
subclass of: function
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has part
      some values from: site
textual definition: A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

household
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: collection of humans
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: process
      intersection of: Restriction
        on property: realizes
        some values from: residence function
subclass of: material entity
subclass of: Restriction
  on property: has member
  some values from: Homo sapiens
textual definition: A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

employee role
type: Class
subclass of: human role within an organization
subclass of: Restriction
  on property: concretizes
  some values from: Class
    intersection of: socio-legal generically dependent continuant
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: declaration
        intersection of: Restriction
definition editor: Amanda hicks
alternative term: employee
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

US Census reference person role
type: Class
subclass of: human social role
subclass of: Restriction
  on property: realized in
  some values from: documenting
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: member of
      some values from: household
textual definition: A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person.
definition editor: Amanda Hicks
definition source: http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

socio-legal human social role
type: Class
subclass of: human social role
subclass of: Restriction
  on property: concretizes
  some values from: socio-legal generically dependent continuant
definition editor: A role that concretizes a socio-lega generically dependent continuant
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

human role within an organization
type: Class
subclass of: socio-legal human social role
subclass of: Restriction
  on property: concretizes
  some values from: Class
    intersection of: socio-legal generically dependent continuant
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: declaration
        intersection of: Restriction
textual definition: A socio-legal human social role that concretizes a socio-legally generically dependent continuat that was created by a declaration performed by an organization.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

employer role
type: Class
subclass of: role in human social processes
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

payer role
type: Class
subclass of: role in human social processes
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

party to an insurance policy
type: Class
subclass of: party to a legal agreement
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

US Census unemployed role
type: Class
subclass of: human social role
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: A US Census unemployed role is a human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff.

US physician assistant role
type: Class
subclass of: health care provider role
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
textual definition: A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

anesthesiologist role
type: Class
subclass of: physician role
textual definition: A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

surgeon role
type: Class
subclass of: physician role
subclass of: Restriction
  on property: realized in
  some values from: surgery
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

neurosurgereon role
type: Class
subclass of: surgeon role
textual definition: A surgeon role realized by its bearer using performing neurosurgery.
imported from: The Ontology of Medically Related Social Entities
imported from: OPMI: Ontology of Precision Medicine and Investigation

individual plan insurance (paid by the member)
type: Class
subclass of: health insurance plan
imported from: OPMI: Ontology of Precision Medicine and Investigation

group plan insurance through employee union
type: Class
subclass of: health insurance plan
imported from: OPMI: Ontology of Precision Medicine and Investigation

USA government health plan insurance
type: Class
subclass of: health insurance plan
imported from: OPMI: Ontology of Precision Medicine and Investigation

no insurance status
type: Class
subclass of: health insurance plan
imported from: OPMI: Ontology of Precision Medicine and Investigation

month of year
type: Class
subclass of: one-dimensional temporal region
imported from: OPMI: Ontology of Precision Medicine and Investigation

January
type: Class
subclass of: month of year
textual definition: The first month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

February
type: Class
subclass of: month of year
textual definition: The second month of the year in the Gregorian calendar.
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

March
type: Class
subclass of: month of year
textual definition: The third month of the year in the Gregorian calendar.
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

April
type: Class
subclass of: month of year
textual definition: The4th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

May
type: Class
subclass of: month of year
textual definition: The 5th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

June
type: Class
subclass of: month of year
textual definition: The 6th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

July
type: Class
subclass of: month of year
textual definition: The 7th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

August
type: Class
subclass of: month of year
textual definition: The 8th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

September
type: Class
subclass of: month of year
textual definition: The 9th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

October
type: Class
subclass of: month of year
textual definition: The 10th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

November
type: Class
subclass of: month of year
textual definition: The 11th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

December
type: Class
subclass of: month of year
textual definition: The 12th month of the year in the Gregorian calendar
definition source: https://en.wikipedia.org/wiki/Gregorian_calendar
imported from: OPMI: Ontology of Precision Medicine and Investigation

day of week
type: Class
subclass of: one-dimensional temporal region
textual definition: A day of a calendar week that includes covers 24 hours each day.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Monday
type: Class
subclass of: day of week
textual definition: The first day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Tuesday
type: Class
subclass of: day of week
textual definition: The second day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Wednesday
type: Class
subclass of: day of week
textual definition: The third day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Thursday
type: Class
subclass of: day of week
textual definition: The fourth day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Friday
type: Class
subclass of: day of week
textual definition: The fifth day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Saturday
type: Class
subclass of: day of week
textual definition: The 6th day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

Sunday
type: Class
subclass of: day of week
textual definition: The 7th day of the week.
definition source: https://en.wikipedia.org/wiki/Week
imported from: OPMI: Ontology of Precision Medicine and Investigation

day of birth
type: Class
subclass of: one-dimensional temporal region
textual definition: A day when an organism (e.g., a human) is born.
definition editor: Oliver He
alternative term: birth date
imported from: OPMI: Ontology of Precision Medicine and Investigation

birthday
type: Class
subclass of: one-dimensional temporal region
textual definition: the anniversary of the birth of a person
definition editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Birthday
imported from: OPMI: Ontology of Precision Medicine and Investigation
comment: There is a difference between birthday and birthdate: The former, such as February 29, occurs each year, while the latter is the exact date a person was born (e.g., January 15, 2001).

personal information
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: Homo sapiens
textual definition: information associated with an individual
definition editor: Oliver He
definition source: https://www.oic.qld.gov.au/guidelines/for-government/access-and-amendment/introduction-to-the-acts/what-is-personal-information
imported from: OPMI: Ontology of Precision Medicine and Investigation

health insurance plan
type: Class
subclass of: personal information
imported from: OPMI: Ontology of Precision Medicine and Investigation
term mapping to NCIT ID: NCIT_C16745
term mapping to UMLS CUI: C0021672

Medicaid
type: Class
subclass of: USA government health plan insurance
textual definition: A joint federal and state program that helps with medical costs for some people with limited income and resources.
definition source: https://en.wikipedia.org/wiki/Medicaid
imported from: OPMI: Ontology of Precision Medicine and Investigation

Medicare
type: Class
subclass of: USA government health plan insurance
textual definition: Medicare is a national health insurance program in the United States, begun in 1966 under the Social Security Administration and now administered by the Centers for Medicare and Medicaid Services (CMS).
definition source: https://en.wikipedia.org/wiki/Medicare_(United_States)
imported from: OPMI: Ontology of Precision Medicine and Investigation

private health insurance plan
type: Class
subclass of: health insurance plan
imported from: OPMI: Ontology of Precision Medicine and Investigation

worker compensation insurance plan
type: Class
subclass of: health insurance plan
imported from: OPMI: Ontology of Precision Medicine and Investigation

visit date
type: Class
subclass of: one-dimensional temporal region
textual definition: the date on which a visit occurs
definition editor: Oliver He
imported from: OPMI: Ontology of Precision Medicine and Investigation
term mapping to NCIT ID: NCIT_C83031
term mapping to UMLS CUI: C1320303

year
type: Class
subclass of: one-dimensional temporal region
imported from: OPMI: Ontology of Precision Medicine and Investigation

medical history information provider role
type: Class
subclass of: health care provider role
textual definition: A role of a person (e.g., a study participant, participant's family member, or participant's physician) who provides the medical history information.
definition editor: Edison Ong, Oliver He
imported from: OPMI: Ontology of Precision Medicine and Investigation

study participant's family member role
type: Class
subclass of: role in human social processes
textual definition: A role of a person who is a family member of a participant in an investigation study.
definition editor: Edison Ong, Oliver He
imported from: OPMI: Ontology of Precision Medicine and Investigation

study participant's physician role
type: Class
subclass of: physician role
textual definition: a role of a physician who takes care of a study participant
definition editor: Edison Ong, Oliver He
imported from: OPMI: Ontology of Precision Medicine and Investigation

quality
type: Class
subclass of: specifically dependent continuant
textual definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: pato.owl
OBO foundry unique label: quality (PATO)
has_alternative_id: PATO:0000072
has exact synonym: trait
has_obo_namespace: quality
id: PATO:0000001

age
type: Class
subclass of: time
textual definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000011
in subset: attribute slim
in subset: scalar slim

frequency
type: Class
subclass of: rate of occurence
textual definition: A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000044
in subset: attribute slim
in subset: scalar slim

biological sex
type: Class
subclass of: organismal quality
textual definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000047
in subset: attribute slim

qualitative
type: Class
subclass of: quality
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000068
comment: TODO: define this or obsolete it and move children somewhere else.

deviation (from_normal)
type: Class
subclass of: qualitative
textual definition: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000069
in subset: attribute slim

position
type: Class
subclass of: physical quality
textual definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: location
has exact synonym: placement
has exact synonym: relational spatial quality

rate
type: Class
subclass of: physical quality of a process
textual definition: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000161
in subset: attribute slim
in subset: scalar slim

time
type: Class
subclass of: physical quality
textual definition: A quality in which events occur in sequence.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000165
in subset: attribute slim
in subset: scalar slim

increased frequency
type: Class
subclass of: frequency
subclass of: increased rate
textual definition: A frequency which is relatively high.
imported from: pato.owl
is opposite of: decreased frequency
has exact synonym: high frequency
has_obo_namespace: quality
has_related_synonym: frequent
id: PATO:0000380
in subset: mpath slim
in subset: value slim

decreased frequency
type: Class
subclass of: frequency
subclass of: decreased rate
textual definition: A frequency which is relatively low.
imported from: pato.owl
is opposite of: increased frequency
has exact synonym: low frequency
has_obo_namespace: quality
has_related_synonym: infrequent
id: PATO:0000381
in subset: mpath slim
in subset: value slim

decreased rate
type: Class
subclass of: rate
subclass of: decreased process quality
textual definition: A rate which is relatively low.
imported from: pato.owl
is opposite of: increased rate
has exact synonym: slow rate
has_obo_namespace: quality
id: PATO:0000911
in subset: mpath slim
in subset: value slim

increased rate
type: Class
subclass of: rate
subclass of: increased process quality
textual definition: A rate which is relatively high.
imported from: pato.owl
is opposite of: decreased rate
has exact synonym: fast rate
has exact synonym: high rate
has_obo_namespace: quality
id: PATO:0000912
in subset: mpath slim
in subset: value slim

physical quality
type: Class
subclass of: physical object quality
textual definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: pato.owl
has_alternative_id: PATO:0002079
database_cross_reference: Wikipedia:Physical_property
has exact synonym: relational physical quality
has_obo_namespace: quality
id: PATO:0001018
in subset: attribute slim

process quality
type: Class
subclass of: quality
textual definition: A quality which inheres in an process.
imported from: pato.owl
has_alternative_id: PATO:0001239
has_alternative_id: PATO:0001240
has exact synonym: quality of a process
has exact synonym: quality of occurrent
has exact synonym: quality of process
has exact synonym: relational quality of occurrent
has_obo_namespace: quality
id: PATO:0001236
comment: See comments of relational quality of a physical entity.

physical object quality
type: Class
subclass of: quality
textual definition: A quality which inheres in a continuant.
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: pato.owl
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
database_cross_reference: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has_narrow_synonym: monadic quality of an object
has_narrow_synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

organismal quality
type: Class
subclass of: physical object quality
textual definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001995

physical quality of a process
type: Class
subclass of: process quality
imported from: pato.owl
created by: george
creation date: 2009-06-05T09:16:46Z
has_obo_namespace: quality
id: PATO:0002062
in subset: attribute slim

displaced
type: Class
subclass of: position
textual definition: A positional quality inhering in a bearer by virtue the bearer's being changed in position.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

increased quality
type: Class
subclass of: deviation (from_normal)
textual definition: A quality that has a value that is increased compared to normal or average.
imported from: pato.owl
is opposite of: decreased quality
created by: George Gkoutos
creation date: 2011-06-16T06:39:43Z
has_obo_namespace: quality
id: PATO:0002300

decreased quality
type: Class
subclass of: deviation (from_normal)
textual definition: A quality that has a value that is decreased compared to normal or average.
imported from: pato.owl
is opposite of: increased quality
created by: George Gkoutos
creation date: 2011-06-16T06:40:15Z
has_obo_namespace: quality
id: PATO:0002301

decreased process quality
type: Class
subclass of: process quality
subclass of: decreased quality
textual definition: A quality of a process that has a value that is decreased compared to normal or average.
imported from: pato.owl
is opposite of: increased process quality
created by: George Gkoutos
creation date: 2011-06-16T06:50:59Z
has_obo_namespace: quality
id: PATO:0002302

increased process quality
type: Class
subclass of: process quality
subclass of: increased quality
textual definition: A quality of a process that has a value that is increased compared to normal or average.
imported from: pato.owl
is opposite of: decreased process quality
created by: George Gkoutos
creation date: 2011-06-16T06:53:08Z
has_obo_namespace: quality
id: PATO:0002304

normal rate
type: Class
subclass of: rate
subclass of: normal process quality
textual definition: A rate which is relatively normal.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0045000
in subset: mpath slim
in subset: value slim

normal process quality
type: Class
subclass of: process quality
textual definition: A quality of aprocess that has a value that is normal or average.
imported from: pato.owl
created by: Luke Slater
creation date: 2017-12-21T14:11:01Z
has_obo_namespace: quality
id: PATO:0045073

normal frequency
type: Class
subclass of: frequency
subclass of: normal rate
textual definition: A frequency which is relatively normal.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0045087
in subset: mpath slim
in subset: value slim

rate of occurence
type: Class
subclass of: rate
textual definition: The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute)
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0050000

collection of organisms
type: Class
subclass of: object aggregate
subclass of: material entity
subclass of: organismal entity
textual definition: A material entity that consists of two or more organisms, viruses, or viroids.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

ecological community
type: Class
subclass of: community
subclass of: multi-species collection of organisms
textual definition: A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
in subset: envoPolar

community
type: Class
subclass of: collection of organisms
textual definition: A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

multi-species collection of organisms
type: Class
subclass of: collection of organisms
textual definition: A collection of organisms that consists of two or more organisms from at least two species.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

organismal entity
type: Class
equivalent class: Class
  union of: organism or virus or viroid
  union of: collection of organisms
subclass of: material entity
textual definition: A material entity that is one or more organisms, viruses or viroids.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

plant anatomical entity
type: Class
subclass of: material entity
textual definition: An anatomical entity that is or was part of a plant.
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation
has exact synonym: entidad anat&#243mica vegetal (Spanish, exact)
has exact synonym: 植物 解剖学（形態）的実体 (Japanese, exact)

system
type: Class
subclass of: material entity
textual definition: A material entity consisting of multiple components that are causally integrated.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
definition editor: Chris Mungall
definition source: http://www.jbiomedsem.com/content/4/1/43
imported from: envo.owl
imported from: OPMI: Ontology of Precision Medicine and Investigation

transportation system
type: Class
subclass of: system
subclass of: Restriction
  on property: has part
  some values from: vehicle
textual definition: A system used for transportation

vehicle
type: Class
subclass of: material entity
subclass of: Restriction
  on property: part of
  some values from: transportation system
textual definition: Guided or unguided devices for carrying persons or freight on land, at sea or in the air. (Source: TRT SN)
definition editor: YOH
definition source: https://en.wikipedia.org/wiki/Vehicle
TRT cross-reference: https://trt.trb.org/trt.asp

car
type: Class
subclass of: ground vehicle
subclass of: Restriction
  on property: has quality
  some values from: motorized

human transportation
type: Class
subclass of: transportation
subclass of: Restriction
  on property: has input
  some values from: passenger
subclass of: Restriction
  on property: has start time
  some values from: timestamp
subclass of: Restriction
  on property: has start location
  some values from: transit stop
subclass of: Restriction
  on property: has end location
  some values from: transit stop
subclass of: Restriction
  on property: has end time
  some values from: timestamp
subclass of: Restriction
  on property: has passenger
  some values from: Homo sapiens
textual definition: the movement of human from one location to another.
definition editor: Oliver He, Andong Chen, Aditi Misra
definition source: https://en.wikipedia.org/wiki/Transport

passenger
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: passenger role
subclass of: Homo sapiens

passenger role
type: Class
subclass of: role

transportion simulation
type: Class
subclass of: planned process

railroad train
type: Class
subclass of: vehicle
definition editor: YOH
TRT cross-reference: https://trt.trb.org/trt.asp

ground vehicle
type: Class
subclass of: vehicle
definition editor: YOH
TRT cross-reference: https://trt.trb.org/trt.asp

ship
type: Class
subclass of: vehicle
definition editor: YOH
TRT cross-reference: https://trt.trb.org/trt.asp

aircraft
type: Class
subclass of: vehicle
definition editor: YOH
TRT cross-reference: https://trt.trb.org/trt.asp

spacecraft
type: Class
subclass of: vehicle
definition editor: YOH
TRT cross-reference: https://trt.trb.org/trt.asp

amphibious vehicle
type: Class
subclass of: vehicle
textual definition: Flat-bottomed motor vehicle that can travel on land or water. (Source: wordnet.princeton.edu)
definition source: https://en.wikipedia.org/wiki/Amphibious_vehicle
TRT cross-reference: https://trt.trb.org/trt.asp

used car
type: Class
subclass of: car

motor vehicle
type: Class
equivalent class: Restriction
  on property: has quality
  some values from: motorized
subclass of: vehicle
subclass of: Restriction
  on property: has quality
  some values from: motorized
textual definition: a self-propelled vehicle, commonly wheeled, that does not operate on rails (such as trains or trams or 4-wheelers) and is used for the transportation of people or cargo.
definition editor: YOH
alternative term: automotive vehicle
alternative term: motorized vehicle
definition source: https://en.wikipedia.org/wiki/Motor_vehicle

human powered vehicle
type: Class
subclass of: ground vehicle
definition editor: YOH
definition source: https://en.wikipedia.org/wiki/Human-powered_transport
TRT cross-reference: https://trt.trb.org/trt.asp

bicycle
type: Class
subclass of: human powered vehicle
TRT cross-reference: https://trt.trb.org/trt.asp

tricycle
type: Class
subclass of: human powered vehicle
TRT cross-reference: https://trt.trb.org/trt.asp

roadway transportation system
type: Class
subclass of: transportation system
subclass of: Restriction
  on property: has part
  some values from: ground vehicle
subclass of: Restriction
  on property: has part
  some values from: road

road
type: Class
subclass of: material entity

equity
type: Class
subclass of: quality
textual definition: the distribution of impacts (benefits and costs) and whether that distribution is considered fair and appropriate.
definition source: https://www.vtpi.org/equity.pdf

transportation equity
type: Class
subclass of: transportation purpose
definition source: https://www.vtpi.org/equity.pdf

evaluation of transportation equity
type: Class
subclass of: process
definition source: https://www.vtpi.org/equity.pdf

horizontal equity of transportation
type: Class
subclass of: transportation equity
definition source: https://www.vtpi.org/equity.pdf

motorized
type: Class
subclass of: quality

vertical equity of transportation
type: Class
subclass of: transportation equity
definition source: https://www.vtpi.org/equity.pdf

latency in terms of equity
type: Class
subclass of: transportation equity
definition source: https://www.vtpi.org/equity.pdf

horse drawn vehicle
type: Class
subclass of: ground vehicle
TRT cross-reference: https://trt.trb.org/trt.asp

fair allocation of resources
type: Class
subclass of: transportation equity

fair opportunity of accessibility
type: Class
subclass of: transportation equity
alternative term: fair opportunity of accessibility to resources

reduction of adverse effect of transportation
type: Class
subclass of: transportation equity

transportation safety
type: Class
subclass of: reduction of adverse effect of transportation

reduction of environmental pollution
type: Class
subclass of: reduction of adverse effect of transportation

participation of all stakeholders
type: Class
subclass of: transportation equity

fair allocation of infrastructure
type: Class
subclass of: fair allocation of resources

fair allocation of service
type: Class
subclass of: fair allocation of resources

fair allocation of expenditure
type: Class
subclass of: fair allocation of resources

fair allocation of roadway
type: Class
subclass of: fair allocation of infrastructure

fair allocation of facilities
type: Class
subclass of: fair allocation of infrastructure

fair allocation of bus stop
type: Class
subclass of: fair allocation of infrastructure

fair allocation of transit station
type: Class
subclass of: fair allocation of infrastructure

fair opportunity of mobility
type: Class
subclass of: fair opportunity of accessibility

fair opportunity of proximity
type: Class
subclass of: fair opportunity of accessibility

fair opportunity of connectivity
type: Class
subclass of: fair opportunity of accessibility

transit desert
type: Class
subclass of: quality
subclass of: Restriction
  on property: has part
  some values from: transit stop
subclass of: Restriction
  on property: has characteristics
  some values from: low accessibility of transit
textual definition: A transit desert is an area with limited transportation supply. Transit deserts are generally characterized by poor public transportation options and possibly poor bike, sidewalk, or road infrastructure.[3] The lack of transportation options present in transit deserts may have negative effects of people’s health, job prospects, and economic mobility.
definition editor: Aditi Misra, Andong Chen, Edison Ong, Oliver He
definition source: https://en.wikipedia.org/wiki/Transit_desert

high accessibility of transit
type: Class
subclass of: accessibility of transit

transit
type: Class
subclass of: transportation
textual definition: contains bus, subway, ...

transportation data
type: Class
subclass of: data item

transportation supply data
type: Class
subclass of: transportation data

transportation demand data
type: Class
subclass of: transportation data

number of bus stops
type: Class
subclass of: transportation supply data

transportation frequency
type: Class
subclass of: transportation supply data

transportation coverage
type: Class
subclass of: transportation supply data

number of household who needs to drive
type: Class
subclass of: transportation demand data

sidewalk and bike route
type: Class
subclass of: transportation supply data

number of transit dependents
type: Class
subclass of: transportation demand data

accessibility of transit
type: Class
subclass of: transportation data
textual definition: A transportation data that represent the accessbility of a transit to the neighboring passages

low accessibility of transit
type: Class
subclass of: accessibility of transit

number of people who need transportation
type: Class
subclass of: transportation supply data

no of drivers - no of young adult below 16
type: Class
subclass of: number of people who need transportation

no of transit-dependent population
type: Class
subclass of: transportation demand data

reason for traveling
type: Class
subclass of: information content entity

home based work
type: Class
subclass of: reason for traveling

moderate accessibility of transit
type: Class
subclass of: accessibility of transit

bus
type: Class
subclass of: vehicle
textual definition: a road vehicle designed to carry many passengers.
definition source: https://en.wikipedia.org/wiki/Bus

transportation purpose
type: Class
subclass of: objective specification

transit stop
type: Class
subclass of: site

transit start stop
type: Class
subclass of: transit stop

transit end stop
type: Class
subclass of: transit stop

bus stop
type: Class
subclass of: transit stop

public transportation
type: Class
subclass of: human transportation

timestamp
type: Class
subclass of: zero-dimensional temporal region
textual definition: A timestamp is a sequence of characters or encoded information identifying when a certain event occurred, usually giving date and time of day, sometimes accurate to a small fraction of a second.
definition editor: Andong Chen, Aditi Misra, Oliver He

anatomical entity
type: Class
subclass of: independent continuant
subclass of: material entity
textual definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
imported from: envo.owl
imported from: OAE: Ontology of Adverse Events
imported from: OPMI: Ontology of Precision Medicine and Investigation
imported from: uberon.owl
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1515976
database_cross_reference: C12219
database_cross_reference: birnlex 6
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FBbt_root:00000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has_obo_namespace: uberon
id: UBERON:0001062
in subset: upper level

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

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.

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
has curation status: pending final vetting
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

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: 2019-11-12

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
creator: Mathias Brochhausen
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.

envo.owl
creator: http://orcid.org/0000-0002-8343-612X
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 186 Logical Axioms: 30]
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6]
creator: http://orcid.org/0000-0002-4366-3088
creator: http://orcid.org/0000-0003-1604-1512
creator: http://orcid.org/0000-0002-6601-2165
comment: Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 132 Logical Axioms: 23]
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.
creator: https://orcid.org/0000-0002-6962-2807

OAE: Ontology of Adverse Events
creator: Desikan Jagannathan
subject: An ontology for the annotation of the adverse event domain.
version info: Vision Release; 1.2.19
Contributor: Elizabeth Blair
creator: "Asiyah" Yu Lin
creator: Abra Guo
Contributor: Sydni Joubran
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: 2019-2-21
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: Cornelius Rosse
creator: Richard Scheuermann
creator: Anand Kumar
creator: Barry Smith
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).

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
creator: Amanda Hicks
version info: 2017-06-08
creator: Mathias Brochhausen
creator: Swetha Garimalla
Contributor: Daniel Welch
creator: Shariq Tariq

OPMI: Ontology of Precision Medicine and Investigation
creator: Asiyah Yu Lin
creator: Yongqun "Oliver" He (YH)
creator: Jie Zheng
creator: Jennifer Schaub
version info: Vision Release: 1.0.97
subject: OPMI subject: Precision medicine and related investigations
license: http://creativecommons.org/licenses/by/4.0/
Format: OWL-DL
Contributor: Matthias Kretzler
Contributor: Sean Mooney
creator: Fred Dowd
creator: Qingliang Leon Li
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 F. O’Toole
date: 1-31-2020
Contributor: Becky Steck
creator: Hong Yu

OBO Relations Ontology
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
Source: ro
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]