LifO: Life Ontology
type: Ontology
date: 03-11-2018
description: LifO is a formal ontology that represents the life processes of organisms and related entities and relations. LifO is a general purpose ontology that covers the common features associated with different types of organisms such as unicellular prokaryotes (e.g., E. coli) and multicellular organisms (e.g., humans).
subject: LifO: An ontology of the life of an organism
Format: OWL-DL
comment: Reference: He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis towards integrative pharmacovigilance research. Current Pharmacology Reports. 2016 Jun;2(3):113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564.
version info: Vision Release: 1.0.17
creator: Yongqun "Oliver" He (YH)

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

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

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

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

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

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

editor note
type: AnnotationProperty
database_cross_reference: IAO:0000116
id: editor_note
shorthand: editor_note
is metadata tag: true
has_obo_namespace: uberon
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: editor note
has curation status: ready for release

term editor
type: AnnotationProperty
label: definition editor
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 source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor: PERSON:Daniel Schober
editor preferred label: term editor
has curation status: ready for release

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

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

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

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

expand expression to
type: AnnotationProperty

OBO foundry unique label
type: AnnotationProperty
has curation status: pending final vetting

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

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

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

has literature mining keywords
type: AnnotationProperty
term editor: Yongqun He
definition: an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition.

synonym
type: AnnotationProperty

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

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

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

is direct form of
type: AnnotationProperty
creator: Chris Mungall
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'
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
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

external_definition
type: AnnotationProperty
definition: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000001
shorthand: external_definition
id: external_definition
is metadata tag: true
has_obo_namespace: uberon

external_ontology_notes
type: AnnotationProperty
definition: Notes on how similar or equivalent classes are represented in other ontologies.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000012
shorthand: external_ontology_notes
id: external_ontology_notes
is metadata tag: true
has_obo_namespace: uberon

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

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

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

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

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

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

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

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

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

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

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

label
type: AnnotationProperty
editor preferred label: label

part of
type: ObjectProperty
type: TransitiveProperty
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
definition: a core relation that holds between a part and its whole
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)
alternative term: part_of
example of usage: this day is part of this year (occurrent parthood)
inverse of: has part
temporal interpretation: axiom holds for all times
sub property of: overlaps
imported from: Ontology for Biomedical Investigation
imported from: OBO Relations Ontology
equivalent property:
  inverse of: has part

has part
type: ObjectProperty
type: TransitiveProperty
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
definition: a core relation that holds between a whole and its part
editor preferred label: has part
alternative term: has_part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
temporal interpretation: axiom holds for all times
sub property of: overlaps
imported from: Ontology for Biomedical Investigation
imported from: OBO Relations Ontology
equivalent property:
  inverse of: part of

inheres in at all times
type: ObjectProperty

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

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

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

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

precedes
type: ObjectProperty
type: TransitiveProperty
editor preferred label: precedes
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.
in_subset: ro-eco
domain: occurrent
range: occurrent
sub property of: temporally related to
imported from: OBO Relations Ontology
property chain axiom: part of
property chain axiom: happens during

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

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

occupies spatial region at some time
type: ObjectProperty

exists at
type: ObjectProperty

has occurrent part
type: ObjectProperty
type: TransitiveProperty

has spatial occupant at some time
type: ObjectProperty

part of occurrent
type: ObjectProperty
type: TransitiveProperty

has disposition at all times
type: ObjectProperty

has participant at all times
type: ObjectProperty

specifically depends on at some time
type: ObjectProperty

part of continuant at some time
type: ObjectProperty

has continuant part at some time
type: ObjectProperty

part of continuant at all times that whole exists
type: ObjectProperty
type: TransitiveProperty

has continuant part at all times that part exists
type: ObjectProperty
type: TransitiveProperty

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

has life blueprint
type: ObjectProperty
definition: An object property that represents a relation between a life process and its genetic design stored in the genotype of an organism

blueprint for phenotype
type: ObjectProperty
term editor: Oliver He
definition: An object property that represents a relation between a genotype and a phenotype where the genotype is the blueprint of the phenotype.

motivated by
type: ObjectProperty
definition: An object property that represents a relation between a life process and a life motive.
term editor: Oliver He

has motive
type: ObjectProperty
definition: An object property that represents a relation between a living organism and a life motive.
term editor: Oliver He

protein has gene template
type: ObjectProperty
definition: An object property that represents a relation between a protein and a gene such that the gene codes for the protein.
term editor: Oliver He

transcribed to
type: ObjectProperty
term editor: Oliver He
definition: An object property that represents a relation between a gene and a RNA such that the gene is transcribed into the RNA.

translated to
type: ObjectProperty
definition: An object property that represents a relation between a mRNA and a protein such that the mRNA is transcribed into the protein.

protein has mRNA template
type: ObjectProperty
definition: An object property that represents a relation between a protein and a mRNA such that the mRNA is translated to the protein.

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

inheres in
type: ObjectProperty
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor preferred label: inheres in
alternative term: inheres_in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
inverse of: bearer of
temporal interpretation: axiom holds for all times
sub property of: inheres in part of
imported from: Ontology for Biomedical Investigation
imported from: OBO Relations Ontology
equivalent property:
  inverse of: bearer of

bearer of
type: ObjectProperty
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor preferred label: bearer of
alternative term: bearer_of
alternative term: is bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
range: specifically dependent continuant
temporal interpretation: axiom holds for all times
imported from: Ontology for Biomedical Investigation
imported from: OBO Relations Ontology
equivalent property:
  inverse of: inheres in

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

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

has role
type: ObjectProperty

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

has component process
type: ObjectProperty
creation date: 2017-05-24T09:49:21Z
created by: dos
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.
sub property of: has component
imported from: OBO Relations Ontology

has effector activity
type: ObjectProperty
type: FunctionalProperty
creation date: 2017-09-22T14:14:36Z
created by: dos
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
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.
sub property of: has component activity
sub property of: regulates
imported from: OBO Relations Ontology

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

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

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

during which ends
type: ObjectProperty
term editor: David Osumi-Sutherland
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.
in_subset: ro-eco
inverse of: ends during
sub property of: temporally related to
imported from: OBO Relations Ontology

encompasses
type: ObjectProperty
type: TransitiveProperty
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.
alternative term: di
term editor: David Osumi-Sutherland
sub property of: during which starts
inverse of: happens during
imported from: OBO Relations Ontology

ends after
type: ObjectProperty
type: TransitiveProperty
term editor: David Osumi-Sutherland
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
in_subset: ro-eco
sub property of: temporally related to
imported from: OBO Relations Ontology
property chain axiom: ends during
property chain axiom: preceded by

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

during which starts
type: ObjectProperty
term editor: David Osumi-Sutherland
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.
in_subset: ro-eco
inverse of: starts during
sub property of: temporally related to
imported from: OBO Relations Ontology

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

immediately precedes
type: ObjectProperty
alternative term: ends_at_start_of
alternative term: meets
term editor: David Osumi-Sutherland
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
in_subset: ro-eco
is direct form of: precedes
sub property of: precedes
imported from: OBO Relations Ontology
property chain axiom: ends with
property chain axiom: starts with

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

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

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

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

has component
type: ObjectProperty
curator notes: 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.
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.
in_subset: ro-eco
sub property of: has part
has curation status: pending final vetting
temporal interpretation: axiom holds for all times
imported from: OBO Relations Ontology

regulates
type: ObjectProperty
type: TransitiveProperty
elucidation: false
term editor: David Hill
term editor: Tanya Berardini
curator notes: Regulation precludes parthood; the regulatory process may not be within the regulated process.
term editor: Chris Mungall
OBO foundry unique label: regulates (processual)
definition source: GO
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: 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.
domain: process
range: process
has curation status: pending final vetting
inverse of: regulated by
sub property of: causally upstream of
imported from: OBO Relations Ontology
definition source: causal-relations
property chain axiom: ends with
property chain axiom: directly regulates

negatively regulates
type: ObjectProperty
term editor: Chris Mungall
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.
OBO foundry unique label: negatively regulates (process to process)
has curation status: pending final vetting
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
imported from: OBO Relations Ontology
definition source: causal-relations
property chain axiom: ends with

positively regulates
type: ObjectProperty
type: TransitiveProperty
OBO foundry unique label: positively regulates (process to process)
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.
term editor: Chris Mungall
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
imported from: OBO Relations Ontology
definition source: causal-relations
property chain axiom: negatively regulates
property chain axiom: ends with

temporally related to
type: ObjectProperty
Source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
term editor: Chris Mungall
curator notes: 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.
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
in_subset: ro-eco
domain: occurrent
range: occurrent
has curation status: pending final vetting
imported from: OBO Relations Ontology
definition source: Allen's interval algebra

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

starts with
type: ObjectProperty
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
alternative term: started by
term editor: Chris Mungall
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.
in_subset: ro-eco
sub property of: has part
has curation status: pending final vetting
sub property of: temporally related to
imported from: OBO Relations Ontology

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

ends with
type: ObjectProperty
type: TransitiveProperty
term editor: Chris Mungall
alternative term: finished by
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.
in_subset: ro-eco
sub property of: has part
has curation status: pending final vetting
sub property of: temporally related to
imported from: OBO Relations Ontology

has input
type: ObjectProperty
term editor: Chris Mungall
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.
alternative term: consumes
in_subset: ro-eco
domain: process
range: material entity
has curation status: pending final vetting
sub property of: has participant
inverse of: input of
imported from: OBO Relations Ontology
property chain axiom: starts with

has output
type: ObjectProperty
term editor: Chris Mungall
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.
alternative term: produces
in_subset: ro-eco
has curation status: pending final vetting
sub property of: has participant
inverse of: output of
imported from: OBO Relations Ontology
property chain axiom: ends with

causally upstream of, positive effect
type: ObjectProperty
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
sub property of: causally upstream of
imported from: OBO Relations Ontology

causally upstream of, negative effect
type: ObjectProperty
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
sub property of: causally upstream of
imported from: OBO Relations Ontology

inheres in part of
type: ObjectProperty
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.
term editor: Chris Mungall
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
temporal interpretation: axiom holds for all times
sub property of: depends on
imported from: OBO Relations Ontology
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
property chain axiom: part of
property chain axiom: inheres in

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

functionally related to
type: ObjectProperty
term editor: Chris Mungall
curator notes: This is a grouping relation that collects relations used for the purpose of connecting structure and function
imported from: OBO Relations Ontology

regulated by
type: ObjectProperty
type: TransitiveProperty
definition: inverse of regulates
term editor: Chris Mungall
OBO foundry unique label: regulated by (processual)
in_subset: RO_0002259
range: process
domain: process
sub property of: causally downstream of or within
imported from: OBO Relations Ontology

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

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

input of
type: ObjectProperty
term editor: Chris Mungall
definition: inverse of has input
in_subset: RO_0002259
in_subset: ro-eco
sub property of: participates in
sub property of: functionally related to
imported from: OBO Relations Ontology

output of
type: ObjectProperty
definition: inverse of has output
term editor: Chris Mungall
in_subset: RO_0002259
in_subset: ro-eco
sub property of: participates in
sub property of: functionally related to
imported from: OBO Relations Ontology

has direct input
type: ObjectProperty
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
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.
alternative term: directly consumes
curator notes: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
term editor: Chris Mungall
has curation status: requires discussion
sub property of: has input
imported from: OBO Relations Ontology
property chain axiom: starts with

obsolete has direct output
type: ObjectProperty
deprecated: true
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.
example of usage: translation SubClassOf has_direct_output some protein
term editor: Chris Mungall
alternative term: directly produces
has curation status: requires discussion
imported from: OBO Relations Ontology

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

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

directly activates
type: ObjectProperty
alternative term: directly positively regulates
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
OBO foundry unique label: directly activates (process to process)
term editor: Chris Mungall
has curation status: requires discussion
sub property of: directly positively regulates
imported from: OBO Relations Ontology
definition source: causal-relations

indirectly activates
type: ObjectProperty
type: TransitiveProperty
alternative term: indirectly positively regulates
term editor: Chris Mungall
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
sub property of: positively regulates
is indirect form of: positively regulates
imported from: OBO Relations Ontology
property chain axiom: directly activates
property chain axiom: indirectly inhibits

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

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

causally related to
type: ObjectProperty
definition: This relation groups causal relations between material entities and causal relations between processes
term editor: Chris Mungall
curator notes: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
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…
has curation status: requires discussion
sub property of: related via dependence to
imported from: OBO Relations Ontology

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

immediately causally upstream of
type: ObjectProperty
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.
term editor: Chris Mungall
has curation status: requires discussion
sub property of: immediately precedes
is direct form of: causally upstream of
sub property of: causally upstream of
imported from: OBO Relations Ontology

directly provides input for
type: ObjectProperty
term editor: Chris Mungall
OBO foundry unique label: directly provides input for (process to process)
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
has curation status: requires discussion
sub property of: immediately causally upstream of
sub property of: transitively provides input for
imported from: OBO Relations Ontology
definition source: causal-relations
property chain axiom: obsolete has direct output
property chain axiom: has direct input

transitively provides input for
type: ObjectProperty
type: TransitiveProperty
term editor: Chris Mungall
definition: transitive form of directly_provides_input_for
curator notes: 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')
OBO foundry unique label: transitively provides input for (process to process)
domain: process
range: process
has curation status: requires discussion
sub property of: causally upstream of
imported from: OBO Relations Ontology

causally upstream of or within
type: ObjectProperty
type: TransitiveProperty
alternative term: influences (processual)
term editor: Chris Mungall
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
has_related_synonym: affects
inverse of: causally downstream of or within
sub property of: causal relation between processes
imported from: OBO Relations Ontology

causally downstream of or within
type: ObjectProperty
type: TransitiveProperty
term editor: Chris Mungall
definition: inverse of causally upstream of or within
in_subset: RO_0002259
sub property of: causal relation between processes
imported from: OBO Relations Ontology
definition source: causal-relations

causal relation between processes
type: ObjectProperty
curator notes: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: Chris Mungall
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.
domain: occurrent
range: occurrent
sub property of: causally related to
imported from: OBO Relations Ontology
definition source: causal-relations

depends on
type: ObjectProperty
term editor: Chris Mungall
imported from: OBO Relations Ontology

directly regulates
type: ObjectProperty
term editor: Chris Mungall
OBO foundry unique label: directly regulates (processual)
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.
sub property of: regulates
is direct form of: regulates
sub property of: immediately causally upstream of
imported from: OBO Relations Ontology
definition source: causal-relations

related via dependence to
type: ObjectProperty
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 notes: 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: OBO Relations Ontology

directly positively regulates
type: ObjectProperty
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.
OBO foundry unique label: directly positively regulates (process to process)
sub property of: positively regulates
sub property of: directly regulates
imported from: OBO Relations Ontology
definition source: causal-relations

directly negatively regulates
type: ObjectProperty
OBO foundry unique label: directly negatively regulates (process to process)
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.
sub property of: negatively regulates
sub property of: directly regulates
imported from: OBO Relations Ontology
definition source: causal-relations

entity
type: Class
subclass of: Restriction
  on property: exists at
  some values from: temporal region
BFO OWL specification label: entity
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
BFO CLIF specification label: Entity
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
imported from: bfo.owl
imported from: mfoem.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl
imported from: ino.owl

continuant
type: Class
subclass of: entity
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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]
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
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])
imported from: bfo.owl
imported from: mfoem.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl
imported from: OBO Relations Ontology
imported from: ino.owl

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

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
BFO CLIF specification label: IndependentContinuant
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
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]
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
example of usage: a heart
BFO OWL specification label: ic
example of usage: a chair
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
imported from: bfo.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl
imported from: OBO Relations Ontology
imported from: ino.owl

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

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

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

disposition
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: role
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: role
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
BFO CLIF specification label: Disposition
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89
BFO OWL specification label: disposition
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
example of usage: an atom of element X has the disposition to decay to an atom of element Y
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocitosis and exocitosis
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
imported from: bfo.owl
imported from: mfoem.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: quality
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: quality
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
BFO CLIF specification label: RealizableEntity
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
BFO OWL specification label: realizable
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
imported from: bfo.owl
imported from: mfoem.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl
imported from: OBO Relations Ontology

quality
type: Class
subclass of: specifically dependent continuant
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
BFO OWL specification label: quality
BFO CLIF specification label: Quality
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
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

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: inheres in at all times
  some values from: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
BFO CLIF specification label: SpecificallyDependentContinuant
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
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.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
BFO OWL specification label: sdc
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
imported from: bfo.owl
imported from: mfoem.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl
imported from: OBO Relations Ontology

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

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

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
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: bfo.owl

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

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

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

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

material entity
type: Class
subclass of: independent continuant
BFO OWL specification label: material
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
BFO CLIF specification label: MaterialEntity
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
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.
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
example of usage: the undetached arm of a human being
imported from: bfo.owl
imported from: cl.owl
imported from: envo.owl
imported from: Ontology for Biomedical Investigation
imported from: ogg.owl
imported from: OBO Relations Ontology
imported from: ino.owl

immaterial entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    complement of: material entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    complement of: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: immaterial entity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
imported from: bfo.owl
imported from: ogg.owl
imported from: OBO Relations Ontology

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

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

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

CRISPR RNA
type: Class
subclass of: ribonucleic acid
id: CHEBI:134528
database_cross_reference: PMID:27672148
definition: Small guide RNAs employed for sequence-specific interference with invading nucleic acids by bacteria.
has_obo_namespace: chebi_ontology
has_related_synonym: crRNA
in_subset: 2 STAR
imported from: chebi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
has_related_synonym: (Deoxyribonucleotide)m
has_related_synonym: (Deoxyribonucleotide)n
has_related_synonym: (Deoxyribonucleotide)n+m
database_cross_reference: CAS:9007-49-2
has_alternative_id: CHEBI:13302
id: CHEBI:16991
has_alternative_id: CHEBI:21123
has_alternative_id: CHEBI:33698
has_alternative_id: CHEBI:4291
has_related_synonym: DNA
has_related_synonym: DNAn
has_related_synonym: DNAn+1
has_related_synonym: DNS
has_exact_synonym: Deoxyribonucleic acid
has_related_synonym: Desoxyribonukleinsaeure
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
database_cross_reference: KEGG:C00039
has_obo_namespace: chebi_ontology
has_related_synonym: deoxyribonucleic acids
has_exact_synonym: deoxyribonucleic acids
has_related_synonym: desoxyribose nucleic acid
has_related_synonym: thymus nucleic acid
in_subset: 3 STAR
imported from: chebi.owl

transfer RNA
type: Class
subclass of: ribonucleic acid
definition: A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis.
formula: C10H17O10PR2(C5H8O6PR)n
database_cross_reference: CAS:9014-25-9
has_alternative_id: CHEBI:10652
has_alternative_id: CHEBI:15145
has_alternative_id: CHEBI:15163
has_alternative_id: CHEBI:15164
has_alternative_id: CHEBI:15165
id: CHEBI:17843
database_cross_reference: KEGG:C00066
has_related_synonym: RNA, transfer
has_obo_namespace: chebi_ontology
has_related_synonym: tRNA
has_exact_synonym: transfer RNA
in_subset: 3 STAR
imported from: chebi.owl

ribosomal RNA
type: Class
subclass of: ribonucleic acid
formula: C15H25O16P2R3
has_alternative_id: CHEBI:10636
has_alternative_id: CHEBI:15010
id: CHEBI:18111
definition: RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.
has_exact_synonym: Ribosomal RNA
has_obo_namespace: chebi_ontology
has_related_synonym: rRNA
has_exact_synonym: ribosomal RNA
in_subset: 3 STAR
imported from: chebi.owl

nucleic acid
type: Class
subclass of: material entity
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
id: CHEBI:33696
has_related_synonym: NA
has_related_synonym: Nukleinsaeure
has_related_synonym: Nukleinsaeuren
has_related_synonym: acide nucleique
has_related_synonym: acides nucleiques
has_related_synonym: acido nucleico
has_related_synonym: acidos nucleicos
has_obo_namespace: chebi_ontology
has_exact_synonym: nucleic acids
in_subset: 3 STAR
imported from: chebi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
database_cross_reference: CAS:63231-63-0
id: CHEBI:33697
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
has_related_synonym: RNA
has_related_synonym: RNS
has_related_synonym: Ribonukleinsaeure
has_obo_namespace: chebi_ontology
has_related_synonym: pentosenucleic acids
has_exact_synonym: ribonucleic acid
has_related_synonym: ribonucleic acids
has_exact_synonym: ribonucleic acids
has_related_synonym: ribose nucleic acid
has_related_synonym: yeast nucleic acid
in_subset: 3 STAR
imported from: chebi.owl

messenger RNA
type: Class
subclass of: ribonucleic acid
subclass of: Restriction
  on property: translated to
  some values from: protein
definition: An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation.
id: CHEBI:33699
has_obo_namespace: chebi_ontology
has_related_synonym: mRNA
has_exact_synonym: messenger RNA
has_related_synonym: template RNA
in_subset: 3 STAR
imported from: chebi.owl

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
formula: C10H17O8PR2(C5H8O5PR)n.C10H17O7PR2(C5H8O6PR)n
id: CHEBI:4705
has_exact_synonym: Double-stranded DNA
database_cross_reference: KEGG:C00434
has_obo_namespace: chebi_ontology
in_subset: 3 STAR
imported from: chebi.owl

small nuclear RNA
type: Class
subclass of: ribonucleic acid
definition: A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells.
id: CHEBI:74035
database_cross_reference: PMID:22907602
database_cross_reference: PMID:23070852
database_cross_reference: PMID:23190533
database_cross_reference: PMID:23348838
database_cross_reference: PMID:23394998
database_cross_reference: PMID:23426875
database_cross_reference: PMID:23727230
database_cross_reference: PMID:23740936
has_related_synonym: U-RNA
has_related_synonym: U-RNAs
database_cross_reference: Wikipedia:Small_nuclear_RNA
has_obo_namespace: chebi_ontology
has_related_synonym: small nuclear RNAs
has_related_synonym: small nuclear ribonucleic acid
has_related_synonym: small nuclear ribonucleic acids
has_related_synonym: snRNA
has_related_synonym: snRNAs
in_subset: 3 STAR
imported from: chebi.owl

single-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
formula: C10H19O14P3R2(C5H8O5PR)n
id: CHEBI:9160
database_cross_reference: KEGG:C00271
has_exact_synonym: Single-stranded DNA
has_obo_namespace: chebi_ontology
in_subset: 3 STAR
imported from: chebi.owl

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

environmental feature
type: Class
subclass of: material entity
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.
definition: A material entity which determines an environmental system.
has_obo_namespace: ENVO
id: ENVO:00002297
imported from: envo.owl

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

environmental system
type: Class
subclass of: system
creation date: 2013-09-23T16:04:08Z
definition: A system which has the disposition to environ one or more material entities.
database_cross_reference: EcoLexicon: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.
has_exact_synonym: environment
imported from: envo.owl

ecosystem
type: Class
subclass of: environmental system
comment: This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
definition: An environmental system which includes both living and non-living components.
imported from: envo.owl

reproduction
type: Class
subclass of: biological_process
id: GO:0000003
has_alternative_id: GO:0019952
has_alternative_id: GO:0050876
definition: The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
database_cross_reference: Wikipedia:Reproduction
has_obo_namespace: biological_process
has_exact_synonym: reproductive physiological process
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

cell activation
type: Class
subclass of: cellular process
definition: A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
id: GO:0001775
has_obo_namespace: biological_process
in_subset: goslim pir
imported from: go.owl

adaptive immune response
type: Class
subclass of: immune response
definition: An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
id: GO:0002250
comment: This term was added by GO_REF:0000022.
database_cross_reference: Wikipedia:Adaptive_immune_system
has_exact_synonym: acquired immune response
has_obo_namespace: biological_process
has_exact_synonym: immune memory response
imported from: go.owl

system process
type: Class
subclass of: multicellular organismal process
definition: A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
id: GO:0003008
has_obo_namespace: biological_process
has_exact_synonym: organ system process
imported from: go.owl

muscle system process
type: Class
subclass of: system process
definition: A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers.
id: GO:0003012
has_obo_namespace: biological_process
has_related_synonym: muscle physiological process
imported from: go.owl

circulatory system process
type: Class
subclass of: system process
definition: A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
id: GO:0003013
database_cross_reference: Wikipedia:Circulatory_system
has_obo_namespace: biological_process
in_subset: goslim chembl
in_subset: goslim generic
imported from: go.owl

renal system process
type: Class
subclass of: system process
definition: A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
id: GO:0003014
has_obo_namespace: biological_process
has_exact_synonym: excretory system process
has_related_synonym: kidney system process
imported from: go.owl

respiratory system process
type: Class
subclass of: system process
subclass of: multicellular organismal process
definition: A system process carried out by the organs and tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
id: GO:0003016
has_alternative_id: GO:0010802
has_obo_namespace: biological_process
has_exact_synonym: respiratory gaseous exchange by respiratory system
imported from: go.owl

cellular_component
type: Class
subclass of: material entity
id: GO:0005575
has_alternative_id: GO:0008372
database_cross_reference: NIF_Subcellular:sao-1337158144
database_cross_reference: NIF_Subcellular:sao1337158144
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
definition: The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
has_exact_synonym: cell or subcellular entity
has_exact_synonym: cellular component
has_obo_namespace: cellular_component
has_related_synonym: subcellular entity
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
in_subset: gosubset prok
imported from: go.owl

nucleus
type: Class
subclass of: intracellular membrane-bounded organelle
definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
id: GO:0005634
database_cross_reference: NIF_Subcellular:sao1702920020
database_cross_reference: Wikipedia:Cell_nucleus
has_exact_synonym: cell nucleus
has_obo_namespace: cellular_component
has_narrow_synonym: horsetail nucleus
in_subset: goslim agr
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
imported from: go.owl

cytoplasm
type: Class
subclass of: intracellular part
definition: All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
id: GO:0005737
database_cross_reference: Wikipedia:Cytoplasm
has_obo_namespace: cellular_component
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: goslim yeast
in_subset: gosubset prok
imported from: go.owl

mitochondrion
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: intracellular part
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
id: GO:0005739
database_cross_reference: NIF_Subcellular:sao1860313010
comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)
database_cross_reference: Wikipedia:Mitochondrion
has_obo_namespace: cellular_component
has_exact_synonym: mitochondria
in_subset: goslim agr
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
imported from: go.owl

generation of precursor metabolites and energy
type: Class
subclass of: cellular metabolic process
id: GO:0006091
definition: The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
has_obo_namespace: biological_process
has_broad_synonym: energy pathways
has_related_synonym: intermediary metabolism
has_related_synonym: metabolic energy generation
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
in_subset: gosubset prok
imported from: go.owl

transcription, DNA-templated
type: Class
subclass of: cellular metabolic process
has_exact_synonym: DNA-dependent transcription
has_alternative_id: GO:0006350
id: GO:0006351
has_alternative_id: GO:0061018
has_alternative_id: GO:0061022
definition: The cellular synthesis of RNA on a template of DNA.
database_cross_reference: Wikipedia:Transcription_(genetics)
has_obo_namespace: biological_process
has_broad_synonym: cellular transcription
has_exact_synonym: cellular transcription, DNA-dependent
has_broad_synonym: transcription
has_related_synonym: transcription regulator activity
has_exact_synonym: transcription, DNA-dependent
in_subset: goslim aspergillus
in_subset: goslim metagenomics
in_subset: goslim pombe
in_subset: gosubset prok
imported from: go.owl

translation
type: Class
subclass of: cellular metabolic process
id: GO:0006412
has_alternative_id: GO:0006416
has_alternative_id: GO:0006453
has_alternative_id: GO:0043037
database_cross_reference: Reactome:REACT_100338
database_cross_reference: Reactome:REACT_100851
database_cross_reference: Reactome:REACT_101045
database_cross_reference: Reactome:REACT_101324
database_cross_reference: Reactome:REACT_1014
database_cross_reference: Reactome:REACT_103420
database_cross_reference: Reactome:REACT_105544
database_cross_reference: Reactome:REACT_29980
database_cross_reference: Reactome:REACT_33559
database_cross_reference: Reactome:REACT_77710
database_cross_reference: Reactome:REACT_79784
database_cross_reference: Reactome:REACT_81734
database_cross_reference: Reactome:REACT_81833
database_cross_reference: Reactome:REACT_82171
database_cross_reference: Reactome:REACT_83429
database_cross_reference: Reactome:REACT_83530
database_cross_reference: Reactome:REACT_86996
database_cross_reference: Reactome:REACT_95535
database_cross_reference: Reactome:REACT_96394
definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
database_cross_reference: Wikipedia:Translation_(genetics)
has_obo_namespace: biological_process
has_exact_synonym: protein anabolism
has_exact_synonym: protein biosynthesis
has_exact_synonym: protein biosynthetic process
has_exact_synonym: protein formation
has_exact_synonym: protein synthesis
has_exact_synonym: protein translation
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

ATP biosynthetic process
type: Class
subclass of: generation of precursor metabolites and energy
has_exact_synonym: ATP anabolism
has_exact_synonym: ATP biosynthesis
has_exact_synonym: ATP formation
has_narrow_synonym: ATP regeneration
has_exact_synonym: ATP synthesis
id: GO:0006754
has_alternative_id: GO:0006758
has_alternative_id: GO:0006759
database_cross_reference: Reactome:REACT_102219
database_cross_reference: Reactome:REACT_104315
database_cross_reference: Reactome:REACT_105384
database_cross_reference: Reactome:REACT_106830
database_cross_reference: Reactome:REACT_109466
database_cross_reference: Reactome:REACT_190
database_cross_reference: Reactome:REACT_28537
database_cross_reference: Reactome:REACT_31626
database_cross_reference: Reactome:REACT_33014
database_cross_reference: Reactome:REACT_78557
database_cross_reference: Reactome:REACT_86305
database_cross_reference: Reactome:REACT_88682
database_cross_reference: Reactome:REACT_90150
database_cross_reference: Reactome:REACT_92655
database_cross_reference: Reactome:REACT_96844
database_cross_reference: Reactome:REACT_991
definition: The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
has_obo_namespace: biological_process
in_subset: gosubset prok
imported from: go.owl

movement of cell or subcellular component
type: Class
subclass of: cellular process
id: GO:0006928
comment: Note that in GO cellular components include whole cells (cell is_a cellular component).
definition: The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
has_obo_namespace: biological_process
has_related_synonym: cell movement
has_exact_synonym: cellular component motion
has_exact_synonym: cellular component movement
in_subset: goantislim grouping
in_subset: gocheck do not annotate
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

chemotaxis
type: Class
subclass of: taxis
id: GO:0006935
definition: The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
database_cross_reference: Wikipedia:Chemotaxis
has_obo_namespace: biological_process
has_exact_synonym: taxis in response to chemical stimulus
in_subset: gosubset prok
imported from: go.owl

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

cell communication
type: Class
subclass of: cellular process
definition: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
id: GO:0007154
database_cross_reference: Wikipedia:Cell_signaling
has_obo_namespace: biological_process
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

behavior
type: Class
subclass of: biological_process
comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
creation date: 2012-09-20T14:06:08Z
id: GO:0007610
has_alternative_id: GO:0044708
definition: The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
database_cross_reference: Wikipedia:Behavior
has_exact_synonym: behavioral response to stimulus
has_exact_synonym: behaviour
has_exact_synonym: behavioural response to stimulus
has_obo_namespace: biological_process
created by: janelomax
has_related_synonym: single-organism behavior
in_subset: gocheck do not manually annotate
in_subset: goslim agr
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

learning
type: Class
subclass of: mental process
definition: Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
id: GO:0007612
database_cross_reference: Wikipedia:Learning
has_obo_namespace: biological_process
imported from: go.owl
imported from: mfoem.owl

feeding behavior
type: Class
subclass of: behavior
definition: Behavior associated with the intake of food.
id: GO:0007631
comment: See also the biological process term 'behavior ; GO:0007610'.
database_cross_reference: Wikipedia:List_of_feeding_behaviours
has_exact_synonym: behavioral response to food
has_exact_synonym: behavioural response to food
has_obo_namespace: biological_process
has_narrow_synonym: drinking
has_narrow_synonym: eating
has_exact_synonym: feeding behaviour
imported from: go.owl

biological_process
type: Class
subclass of: life process
creation date: 2012-09-19T15:05:24Z
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
id: GO:0008150
has_alternative_id: GO:0044699
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_obo_namespace: biological_process
editor preferred label: biological_process
created by: janelomax
has_exact_synonym: physiological process
has_related_synonym: single organism process
has_related_synonym: single-organism process
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
in_subset: gosubset prok
imported from: go.owl
imported from: Ontology for Biomedical Investigation

metabolic process
type: Class
subclass of: biological_process
creation date: 2012-10-17T15:46:40Z
id: GO:0008152
has_alternative_id: GO:0044710
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
definition: The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
database_cross_reference: Wikipedia:Metabolism
has_obo_namespace: biological_process
created by: janelomax
has_narrow_synonym: metabolic process resulting in cell growth
has_exact_synonym: metabolism
has_narrow_synonym: metabolism resulting in cell growth
has_related_synonym: single-organism metabolic process
in_subset: gocheck do not manually annotate
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

energy taxis
type: Class
subclass of: taxis
id: GO:0009453
definition: The directed movement of a motile cell or organism in response to physical parameters involved in energy generation, such as light, oxygen, and oxidizable substrates.
has_obo_namespace: biological_process
has_exact_synonym: energytaxis
has_exact_synonym: taxis in response to energy source
in_subset: gosubset prok
imported from: go.owl

response to external stimulus
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
id: GO:0009605
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has_obo_namespace: biological_process
has_exact_synonym: response to environmental stimulus
in_subset: gocheck do not manually annotate
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

response to endogenous stimulus
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
id: GO:0009719
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has_obo_namespace: biological_process
in_subset: gocheck do not manually annotate
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

cellular process
type: Class
subclass of: biological_process
creation date: 2012-12-11T16:56:55Z
definition: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
has_alternative_id: GO:0008151
id: GO:0009987
has_alternative_id: GO:0044763
has_alternative_id: GO:0050875
has_obo_namespace: biological_process
has_narrow_synonym: cell growth and/or maintenance
has_exact_synonym: cell physiology
has_exact_synonym: cellular physiological process
created by: janelomax
has_related_synonym: single-organism cellular process
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

membrane
type: Class
subclass of: cellular_component
definition: A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
id: GO:0016020
database_cross_reference: Wikipedia:Biological_membrane
has_obo_namespace: cellular_component
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
in_subset: gosubset prok
imported from: go.owl

cell growth
type: Class
subclass of: cellular process
subclass of: growth
id: GO:0016049
has_alternative_id: GO:0048591
definition: The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
has_obo_namespace: biological_process
has_related_synonym: cell expansion
has_exact_synonym: cellular growth
has_exact_synonym: growth of cell
has_related_synonym: metabolic process resulting in cell growth
has_related_synonym: metabolism resulting in cell growth
has_related_synonym: non-developmental cell growth
has_related_synonym: non-developmental growth of a unicellular organism
in_subset: gocheck do not annotate
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

digestive system process
type: Class
subclass of: system process
definition: A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
id: GO:0022600
has_obo_namespace: biological_process
imported from: go.owl

cell differentiation
type: Class
subclass of: cellular developmental process
id: GO:0030154
definition: The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
database_cross_reference: Wikipedia:Cellular_differentiation
has_obo_namespace: biological_process
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim mouse
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

regeneration
type: Class
subclass of: developmental process
id: GO:0031099
definition: The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass).
database_cross_reference: Wikipedia:Regeneration_(biology)
has_obo_namespace: biological_process
imported from: go.owl

multicellular organismal process
type: Class
subclass of: biological_process
creation date: 2012-09-19T16:07:47Z
definition: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
id: GO:0032501
has_alternative_id: GO:0044707
has_alternative_id: GO:0050874
has_obo_namespace: biological_process
created by: janelomax
has_exact_synonym: organismal physiological process
has_related_synonym: single-multicellular organism process
in_subset: goslim pir
imported from: go.owl

developmental process
type: Class
subclass of: biological_process
creation date: 2012-12-19T12:21:31Z
definition: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
id: GO:0032502
has_alternative_id: GO:0044767
has_obo_namespace: biological_process
has_narrow_synonym: development
created by: janelomax
has_related_synonym: single-organism developmental process
in_subset: goslim agr
in_subset: goslim aspergillus
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

organ growth
type: Class
subclass of: multicellular organismal process
subclass of: developmental growth
id: GO:0035265
definition: The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function.
has_obo_namespace: biological_process
imported from: go.owl

growth
type: Class
subclass of: biological_process
id: GO:0040007
has_alternative_id: GO:0048590
comment: See also the biological process term 'cell growth ; GO:0016049'.
definition: The increase in size or mass of an entire organism, a part of an organism or a cell.
has_obo_namespace: biological_process
has_related_synonym: growth pattern
has_related_synonym: non-developmental growth
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok
imported from: go.owl

locomotion
type: Class
subclass of: biological_process
id: GO:0040011
definition: Self-propelled movement of a cell or organism from one location to another.
has_obo_namespace: biological_process
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

taxis
type: Class
subclass of: locomotion
id: GO:0042330
definition: The directed movement of a motile cell or organism in response to an external stimulus.
database_cross_reference: Wikipedia:Taxis
has_obo_namespace: biological_process
has_exact_synonym: directed movement in response to stimulus
in_subset: gosubset prok
imported from: go.owl

eating behavior
type: Class
subclass of: feeding behavior
id: GO:0042755
definition: The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.
has_obo_namespace: biological_process
has_exact_synonym: eating behaviour
imported from: go.owl

drinking behavior
type: Class
subclass of: feeding behavior
id: GO:0042756
definition: The specific behavior of an organism relating to the intake of liquids, especially water.
has_obo_namespace: biological_process
has_exact_synonym: drinking behaviour
imported from: go.owl

organelle
type: Class
subclass of: cellular_component
id: GO:0043226
database_cross_reference: NIF_Subcellular:sao1539965131
definition: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
database_cross_reference: Wikipedia:Organelle
has_obo_namespace: cellular_component
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

intracellular organelle
type: Class
subclass of: organelle
subclass of: intracellular part
id: GO:0043229
definition: Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
has_obo_namespace: cellular_component
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

intracellular membrane-bounded organelle
type: Class
subclass of: organelle
subclass of: intracellular organelle
id: GO:0043231
definition: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
has_obo_namespace: cellular_component
has_exact_synonym: intracellular membrane-enclosed organelle
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

extraorganismal space
type: Class
subclass of: extracellular region part
id: GO:0043245
definition: The environmental space outside of an organism; this may be a host organism in the case of parasitic and symbiotic organisms.
has_obo_namespace: cellular_component
in_subset: gosubset prok
imported from: go.owl

extracellular space of host
type: Class
subclass of: cellular_component
subclass of: extracellular region part
id: GO:0043655
definition: The space within a host but external to the plasma membrane of host cells, e.g. within host bloodstream.
has_obo_namespace: cellular_component
has_exact_synonym: host extracellular space
in_subset: gosubset prok
imported from: go.owl

cellular metabolic process
type: Class
subclass of: metabolic process
subclass of: cellular process
id: GO:0044237
definition: The chemical reactions and pathways by which individual cells transform chemical substances.
has_obo_namespace: biological_process
has_exact_synonym: cellular metabolism
has_related_synonym: intermediary metabolism
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

extracellular region part
type: Class
subclass of: cellular_component
definition: Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite.
id: GO:0044421
database_cross_reference: NIF_Subcellular:sao9117790637
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has_obo_namespace: cellular_component
has_related_synonym: extracellular structure
in_subset: goantislim grouping
in_subset: gocheck do not annotate
in_subset: gosubset prok
imported from: go.owl

intracellular part
type: Class
subclass of: cellular_component
definition: Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
id: GO:0044424
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has_obo_namespace: cellular_component
in_subset: goantislim grouping
in_subset: gocheck do not annotate
in_subset: gosubset prok
imported from: go.owl

innate immune response
type: Class
subclass of: immune response
has_alternative_id: GO:0002226
id: GO:0045087
definition: Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
database_cross_reference: Reactome:REACT_101086
database_cross_reference: Reactome:REACT_108180
database_cross_reference: Reactome:REACT_110518
database_cross_reference: Reactome:REACT_31297
database_cross_reference: Reactome:REACT_32992
database_cross_reference: Reactome:REACT_6802
database_cross_reference: Reactome:REACT_78575
database_cross_reference: Reactome:REACT_81815
database_cross_reference: Reactome:REACT_81962
database_cross_reference: Reactome:REACT_86987
database_cross_reference: Reactome:REACT_88681
database_cross_reference: Reactome:REACT_90618
database_cross_reference: Reactome:REACT_90753
database_cross_reference: Reactome:REACT_94451
database_cross_reference: Reactome:REACT_95471
database_cross_reference: Reactome:REACT_95642
database_cross_reference: Reactome:REACT_99610
comment: This term was improved by GO_REF:0000022. It was moved.
database_cross_reference: Wikipedia:Innate_immune_system
has_obo_namespace: biological_process
has_exact_synonym: innate immunity
has_exact_synonym: nonspecific immune response
imported from: go.owl

developmental growth
type: Class
subclass of: developmental process
subclass of: growth
id: GO:0048589
definition: The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
has_obo_namespace: biological_process
imported from: go.owl

cellular developmental process
type: Class
subclass of: cellular process
subclass of: developmental process
definition: A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
id: GO:0048869
has_obo_namespace: biological_process
in_subset: gosubset prok
imported from: go.owl

cell motility
type: Class
subclass of: movement of cell or subcellular component
subclass of: locomotion
definition: Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
id: GO:0048870
has_obo_namespace: biological_process
has_exact_synonym: cell locomotion
has_related_synonym: cell movement
has_exact_synonym: movement of a cell
in_subset: goslim chembl
in_subset: goslim generic
in_subset: gosubset prok
imported from: go.owl

nervous system process
type: Class
subclass of: system process
definition: A organ system process carried out by any of the organs or tissues of neurological system.
comment: Discussion of class label and synonyms: https://github.com/geneontology/go-ontology/issues/13824
id: GO:0050877
has_obo_namespace: biological_process
has_exact_synonym: neurological system process
has_exact_synonym: neurophysiological process
has_related_synonym: pan-neural process
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim pir
imported from: go.owl

endocrine process
type: Class
subclass of: system process
id: GO:0050886
definition: The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
has_obo_namespace: biological_process
has_exact_synonym: endocrine physiological process
has_exact_synonym: endocrine physiology
in_subset: goslim pir
imported from: go.owl

response to stimulus
type: Class
subclass of: biological_process
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
id: GO:0050896
has_alternative_id: GO:0051869
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has_obo_namespace: biological_process
has_exact_synonym: physiological response to stimulus
in_subset: gocheck do not manually annotate
in_subset: goslim agr
in_subset: goslim mouse
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

biological regulation
type: Class
subclass of: biological_process
definition: Any process that modulates a measurable attribute of any biological process, quality or function.
id: GO:0065007
has_obo_namespace: biological_process
has_broad_synonym: regulation
in_subset: goslim pir
in_subset: gosubset prok
imported from: go.owl

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

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

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

data about an ontology part
type: Class
subclass of: data item
term editor: Person:Alan Ruttenberg
definition: data about an ontology part is a data item about a part of an ontology, for example a term
imported from: mfoem.owl
imported from: Ontology for Biomedical Investigation

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor note: 2/2/2009 is_specified_output of some assay?
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred label: measurement datum
term editor: person:Chris Stoeckert
has curation status: pending final vetting
imported from: Ontology for Biomedical Investigation

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

interaction network process
type: Class
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: interaction
definition: A process that includes at least two associated interactions.
editor note: If the interaction is physical and molecular, the interaction network is molecular interactions usually found in cells.
term editor: YH, ZX
definition source: http://en.wikipedia.org/wiki/Interaction_network
imported from: ino.owl

interaction
type: Class
subclass of: process
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has role
      some values from: interactor role
definition: A process that has two or more participants (i.e., interactors) that have an effect upon one another.
term editor: YH, ZX
has literature mining keywords: interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts
definition source: https://en.wikipedia.org/wiki/Interaction
imported from: ino.owl

pathway process
type: Class
subclass of: interaction network process
subclass of: Restriction
  on property: ends with
  some values from: interaction
subclass of: Restriction
  on property: starts with
  some values from: interaction
definition: an interaction network process that includes at least two related interactions together to achieve one specific task(s). A pathway process has a start point(s) and an end point(s).
term editor: YH, ZX
imported from: ino.owl

Bayesian network
type: Class
subclass of: interaction network model
term editor: YH, ZX
definition: an interaction network model that is represented by a probabilistic graphical model (a type of statistical model) that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG).
definition source: WEB: http://en.wikipedia.org/wiki/Bayesian_network
imported from: ino.owl

regulator role
type: Class
subclass of: interactor role
definition: an regulator role that is borne by a material entity that regulates an interaction.
term editor: YH
imported from: ino.owl

input interactor role
type: Class
subclass of: interactor role
term editor: YH, ZX
alternative term: interaction input role
definition: an interactor role that is borne by a material entity that acts as an input of an interaction.
imported from: ino.owl

output interactor role
type: Class
subclass of: interactor role
alternative term: interaction output role
definition: an interactor role that is borne by a material entity that acts as an output of an interaction.
term editor: YH, ZX
imported from: ino.owl

mutual information network
type: Class
subclass of: interaction network model
definition source: WEB: http://en.wikipedia.org/wiki/Mutual_information
definition: an interaction network model that is represented by at least two mutual information interactions.
term editor: YH, ZX
imported from: ino.owl

node
type: Class
subclass of: object
term editor: YH, ZX
comment: is node equal to interactor?? (YL)
definition: a node is an object that represents an interactor in a graph of an interaction or interaction network.
imported from: ino.owl

edge
type: Class
subclass of: object
term editor: YH, ZX
definition: an edge is an object that represents a graphic line that links two interactors in an interaction.
imported from: ino.owl

interactor role
type: Class
subclass of: role
term editor: YH, ZX
definition: a role that is borne by a material entity to act as a participant in an interaction process.
imported from: ino.owl

motivator role
type: Class
subclass of: input interactor role
definition source: https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory
definition: an input interactor role that is borne by an entity that motivates a life process.
term editor: Oliver He
imported from: ino.owl

hygiene factor role
type: Class
subclass of: input interactor role
term editor: Oliver He
definition: an input interactor role that is borne by an entity (e.g. status, job security, salary and fringe benefits) that does not motivate if present, but, if absent, results in demotivation.
definition source: https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory
imported from: ino.owl

regulation
type: Class
subclass of: association
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has role
      some values from: regulator role
has literature mining keywords: regulate, regulated, regulates, regulating, regulation, regulator, modulate, modulated, modulates, modulating, modulation, mediate, mediated, mediates, mediating, influence, influenced, influences, influencing, affect, affected, affecting, affects, impact, impacted, impacting, impacts, effect, effected, effecting, effects, require, required, requires, requiring, respond, responded, responding, responds, responsive, change, changed, changes, changing, alter, altered, altering, alters, modified, modifies, modify, modifying, depend, depended, depending, depends, direct, directed, directing, directs, drive, driven, drives, driving, cause, caused, causes, causing, lead, leading, leads, led, target, targeted, targeting, targets, dependent, essential for
term editor: YH, ZX, AO, JH
definition: A regulation represents a regulatory interaction between two interactors.
see also: GO: GO_0065007
imported from: ino.owl

interaction network model
type: Class
subclass of: information content entity
definition source: https://en.wikipedia.org/wiki/Interactome
definition: An information content entity that models interaction network
imported from: ino.owl

life
type: Class
subclass of: process
subclass of: Restriction
  on property: has life blueprint
  some values from: genotype
subclass of: Restriction
  on property: has part
  some values from: life process
subclass of: Restriction
  on property: motivated by
  some values from: life motive
subclass of: Restriction
  on property: has participant
  some values from: organism
subclass of: Restriction
  on property: starts with
  some values from: the first cell formation moment
subclass of: Restriction
  on property: has participant
  some values from: environmental system
subclass of: Restriction
  on property: ends with
  some values from: life death moment
definition source: http://www.hegroup.org/onenettheory.html
definition source: https://en.wikipedia.org/wiki/Life
definition: An integrative interaction network process of an organism that starts from the moment when the first cell forms, has its blueprint stored in the genotype, and performs its dynamic process by interacting with its environment to achieve its survival and other motivations.
term editor: Oliver He
definition source: He Y. Ontology-based vaccine and drug adverse event representation and theory-guided systematic causal network analysis towards integrative pharmacovigilance research. Current Pharmacology Reports. 2016 Jun;2(3):113-128. DOI: 10.1007/s40495-016-0055-0. PMID: 27458549. PMCID: PMC4957564.
alternative term: OneNet life

genotype
type: Class
subclass of: material entity
subclass of: Restriction
  on property: part of
  some values from: genome
subclass of: Restriction
  on property: has part
  some values from: gene
subclass of: Restriction
  on property: blueprint for phenotype
  some values from: phenotype
definition: A material entity that is the part (DNA sequence) of the genetic makeup of an cell or organism which determines a specific characteristic (phenotype) of that cell or organism.
term editor: Oliver He

prokaryotic genotype
type: Class
subclass of: genotype
subclass of: Restriction
  on property: part of
  some values from: Class
    union of: Bacteria
    union of: Archaea
definition: a genotype that exists in a prokaryotic organism (bacterium or archaeon).
term editor: Oliver He

eukaryotic genotype
type: Class
subclass of: genotype
subclass of: Restriction
  on property: part of
  some values from: Eukaryota
definition: a genotype that exists in an eukaryotic organism (e.g., human).
term editor: Oliver He

organism
type: Class
equivalent class: Class
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: cell
definition: An organism is an individual entity that exhibits the properties of life, including reproduction, growth and development, maintenance, and response to stimuli. All organisms are composed of one or more cells.
term editor: Oliver He
comment: An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction, growth or metabolism.
definition source: https://en.wikipedia.org/wiki/Organism

the first cell formation moment
type: Class
subclass of: life time point
definition: A time point when the first cell of a multicellular organism or the cell of a single cell organism just forms. This is the time when the OneNet life process of an organism just starts based on the OneNet theory of life.
term editor: Oliver He
alternative term: OneNet life start time

life process
type: Class
subclass of: process
subclass of: Restriction
  on property: part of
  some values from: life
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Life
definition: A process that is performed by a life organism or a component of the life organism.

life motivation
type: Class
subclass of: life process
subclass of: Restriction
  on property: realizes
  some values from: life motive
definition source: https://en.wikipedia.org/wiki/Motivation
term editor: Oliver He
definition: a life process that motivates or stimulates an individual to an action to accomplish a goal or motive.

life motive
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: realized in
  some values from: life motivation
subclass of: Restriction
  on property: inheres in
  some values from: organism
term editor: Oliver He
definition: a realizable entity that represents a need, desire, or drive within an organism that motivates the organism to action.
definition source: https://en.wikipedia.org/wiki/Motivation

motive to survive
type: Class
subclass of: life motive
definition: A life motive to survive. This is the most basic motive of life.
term editor: Oliver He

society
type: Class
subclass of: population
subclass of: Restriction
  on property: has part
  some values from: organism
subclass of: Restriction
  on property: has motive
  some values from: society motive
definition: A society is a group of people who have persistent social interactions , share the same geographical or social territory, and have common motivations.
definition source: https://en.wikipedia.org/wiki/Society
term editor: Oliver He

society motive
type: Class
subclass of: social motive
subclass of: Restriction
  on property: realized in
  some values from: society motivation
definition source: a social motive that is made by a society to achieve.
term editor: Oliver He

physiological need
type: Class
subclass of: life motive
definition: A life motive to physiological need such as hunger, thirst, and sleep.
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
term editor: Oliver He

motive for social belonging
type: Class
subclass of: life motive
definition: A life motive for interpersonal and involves feelings of belongingness.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

motive for self-actualization
type: Class
subclass of: life motive
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
term editor: Oliver He
definition: A life motive for an organism to realize and achieve its full potential.

motive for self-transcendence
type: Class
subclass of: life motive
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
term editor: Oliver He
definition: A life motive for an organism to realize and achieve some higher goal outside oneself, in altruism and spirituality, which is essentially the desire to reach infinite.

motive for self-esteem
type: Class
subclass of: life motive
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
definition: A life motive for an organism to achieve a desire to be accepted and valued by others.
term editor: Oliver He

safety need
type: Class
subclass of: life motive
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
definition: A life motive for safety.

physical safety need
type: Class
subclass of: safety need
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
term editor: Oliver He
definition: A safety need that is on an organism's physical safety.

economical safety need
type: Class
subclass of: safety need
term editor: Oliver He
definition: A safety need that is on an organism's economical situation
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

health need
type: Class
subclass of: safety need
definition: A safety need to maintain one's health and well-being
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
term editor: Oliver He

sleep need
type: Class
subclass of: physiological need
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
definition: A physiological need for sleep.

food need
type: Class
subclass of: physiological need
term editor: Oliver He
definition: A physiological need for food.
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

water need
type: Class
subclass of: physiological need
definition: A physiological need for water or against thirst.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

breathing need
type: Class
subclass of: physiological need
term editor: Oliver He
definition: A physiological need for air and breathing.
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

clothing need
type: Class
subclass of: physiological need
term editor: Oliver He
definition: A physiological need for clothing.
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

shelter need
type: Class
subclass of: physiological need
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
definition: A physiological need for shelter.

sexual instinct need
type: Class
subclass of: physiological need
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
term editor: Oliver He
definition: A physiological need for sexual instinct.

motive for friendship
type: Class
subclass of: motive for social belonging
definition: A social belonging motive for friendship.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

motive for intimacy
type: Class
subclass of: motive for social belonging
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs
definition: A social belonging motive for friendship.
term editor: Oliver He

motive for family
type: Class
subclass of: motive for social belonging
definition: A social belonging motive for family.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Maslow%27s_hierarchy_of_needs

intrinsic motivation
type: Class
subclass of: life motivation
definition source: https://en.wikipedia.org/wiki/Motivation#Intrinsic_motivation
definition: a life motivation that is motivated by intrinsic self-desire to seek out new things and new challenges, to analyze one's capacity, to observe, or to gain knowledge. It is driven by an interest or enjoyment in the task itself, and exists within the individual rather than relying on external pressures or a desire for consideration.
term editor: Oliver He
comment: The phenomenon of intrinsic motivation was first acknowledged within experimental studies of animal behavior. In these studies, it was evident that the organisms would engage in playful and curiosity driven behaviors in the absence of reward.

extrinsic motivation
type: Class
subclass of: life motivation
definition source: https://en.wikipedia.org/wiki/Motivation#Extrinsic_motivation
example of usage: Common extrinsic motivations are rewards (for example money or grades) for showing the desired behavior, and the threat of punishment following misbehavior. Competition is an extrinsic motivator because it encourages the performer to win and to beat others, not simply to enjoy the intrinsic rewards of the activity. A cheering crowd and the desire to win a trophy are also extrinsic incentives.
term editor: Oliver He
definition: a life motivation that is motivated by influences outside of the individual. The performance aims to attain a desired outcome. It is the opposite of intrinsic motivation.

life time point
type: Class
subclass of: zero-dimensional temporal region
term editor: Oliver He
definition: A zero-dimensional temporal region that indicates a specific time point in one organism's life.
alternative term: OneNet life start time

effectiveness
type: Class
subclass of: process profile
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Effectiveness
definition source: http://fusion.isif.org/proceedings/fusion12CD/html/pdf/313_146.pdf
definition: a process profile that represents a process’s capability to produce an effect.

efficiency
type: Class
subclass of: effectiveness
definition: an effectiveness that represents a process’s capability to get a thing done, or meet a target or desire.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Efficacy

correctness
type: Class
subclass of: effectiveness
definition: an effectiveness that represents a process’s capability to do a "right" thing, i.e., setting a right target to achieve an overall goal (the effect).
definition source: https://en.wikipedia.org/wiki/Correctness_(computer_science)
term editor: Oliver He

efficiency
type: Class
subclass of: effectiveness
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Correctness_(computer_science)
definition: an effectiveness that represents a process’s capability to do a thing in the most economical way.

social process
type: Class
subclass of: process
subclass of: Restriction
  on property: occurs in
  some values from: society
definition source: https://www.slideshare.net/annaloucanete7/chapter10-social
definition: A recurrent and patterned process that involves the interactions or responses of indivdiuals to one antoher wihch have attained statiblity.
term editor: Oliver He

scholarly society
type: Class
subclass of: society
subclass of: Restriction
  on property: has part
  some values from: organism
subclass of: Restriction
  on property: has motive
  some values from: society motive
definition: A society that exists to promote an academic discipline, profession, or a group of related disciplines such as the arts.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Learned_society

open society
type: Class
subclass of: society
subclass of: Restriction
  on property: has part
  some values from: organism
subclass of: Restriction
  on property: has motive
  some values from: society motive
term editor: Oliver He
definition: A society in which individuals are confronted with personal decisions as opposed to a magical or tribal or collectivist society.
definition source: https://en.wikipedia.org/wiki/Open_society

cultural change
type: Class
subclass of: social process
alternative term: repositioning of culture
definition source: https://en.wikipedia.org/wiki/Culture_change
term editor: Oliver He
definition: A society process that changes or reconstructs the cultural concept of a society

social behavior
type: Class
subclass of: social process
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Social_behavior
definition: A behavior among two or more organisms in a society.

collective animal behavior
type: Class
subclass of: social behavior
definition source: https://en.wikipedia.org/wiki/Social_behavior
definition: A social behavior that involves the coordinated behavior of large groups of similar animals as well as emergent properties of these groups.
term editor: Oliver He

social consciousness
type: Class
subclass of: social process
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Social_consciousness
definition: A consciousness shared by individuals within a society.

aggressive social behavior
type: Class
subclass of: social behavior
definition source: https://en.wikipedia.org/wiki/Social_behavior
definition: A social behavior that can potentially cause or threaten physical or emotional harm.
term editor: Oliver He

bullying social behavior
type: Class
subclass of: aggressive social behavior
term editor: Oliver He
definition: An aggressive social behavior that involves one bullying another.
alternative term: bullying behavior
definition source: https://en.wikipedia.org/wiki/Social_behavior

violent social behavior
type: Class
subclass of: aggressive social behavior
alternative term: violent behavior
definition source: https://en.wikipedia.org/wiki/Social_behavior
definition: An aggressive social behavior that involves violent actions among individuals.
term editor: Oliver He

culture
type: Class
subclass of: quality
definition: the quality in a society that arises from a concern for what is regarded as excellent in arts, letters, manners, scholarly pursuits, etc.
term editor: Oliver He
definition source: http://www.dictionary.com/browse/culture

social motive
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: realized in
  some values from: social motivation
definition source: An incentive or drive resulting from a sociocultural influence that initiates behavior toward a particular goal.
definition source: https://medical-dictionary.thefreedictionary.com/social+motivation
term editor: Oliver He

social motivation
type: Class
subclass of: social process
subclass of: Restriction
  on property: realizes
  some values from: social motive
definition source: https://www.slideshare.net/annaloucanete7/chapter10-social
definition: A social process that is driven by a social motive.
term editor: Oliver He

society motivation
type: Class
subclass of: social motivation
subclass of: Restriction
  on property: realizes
  some values from: society motive
definition: A social motivation that is driven by a society motive.
definition source: https://www.slideshare.net/annaloucanete7/chapter10-social
term editor: Oliver He

social interaction
type: Class
equivalent class: Class
  intersection of: interaction
  intersection of: social process
subclass of: social process
term editor: Oliver He
definition: An interaction between two or more individuals or populations in a society. Social interaction is a building block of society.
definition source: https://courses.lumenlearning.com/boundless-sociology/chapter/understanding-social-interaction/

social rule
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: realized in
  some values from: social behavior
term editor: Oliver He
definition: a realizable entity, such as norm, law, regulation, that is realized in social behavior.
definition source: https://en.wikipedia.org/wiki/Social_rule_system_theory

social norm
type: Class
subclass of: social rule
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Social_norm
definition: informal understanding that governs the behavior of the members of a society

law
type: Class
subclass of: social rule
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Law
definition: a social rule that is created and enforced through social or governmental institutions to regulate behavior in a society.

life death moment
type: Class
subclass of: life time point
term editor: Oliver He
definition: A time point when a life organism just dies.

life dynamics
type: Class
subclass of: information content entity
alternative term: OneNet life dynamics
definition: A science branch that analyzes the mechanisms of dynamic interactions among different participants and their associated pathways and networks in a life organism.
term editor: Oliver He

emotion process
type: Class
subclass of: mental process
synonym: short-term emotion
synonym: occurrent emotion
definition: An emotion process is a complex mental process that is a synchronized aggregate of constituent mental processes including an appraisal process as part, and which gives rise to an action tendency.
imported from: mfoem.owl

cognitive process
type: Class
subclass of: mental process
subclass of: Restriction
  on property: has participant at all times
  some values from: cognitive representation
definition: A mental process that creates, modifies or has as participant some cognitive representation.
see also: GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.'
imported from: mfoem.owl

consciousness
type: Class
subclass of: process profile
subclass of: mental process
subclass of: Restriction
  on property: part of occurrent
  some values from: Class
    intersection of: mental process
    intersection of: Class
      complement of: consciousness
comment: Note that while there are different modes of consciousness corresponding to the different senses, the whole of conscious experience at any one time is largely experienced as a unity, that is, as a fused whole. Mental processes which are simultaneously ongoing are separable only in fiat, not in essence.
definition: Consciousness is an inseparable part of all mental processes. It is that part of the mental process that: a) confers a subjective perspective, a phenomenology, an experience of the mental process of which it is a part; and b) intends the object or event that the mental process is about, should such exist; i.e., it confers intentionality on the mental process.
imported from: mfoem.owl

perception
type: Class
subclass of: mental process
definition: a mental process which is a) produced by a causal process (for example involving light rays or air vibrations) involving a part of the environment of the organism, and b) is experienced by the organism as being so caused, and c) in which the relevant part of the environment is thereby represented to the organism
imported from: mfoem.owl

mental process
type: Class
subclass of: life process
definition: A mental process is a bodily process that is of a type such that it can of itself be conscious. Examples include thinking, feeling pain, remembering and emotion as occurrent experiences.
see also: GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.'
definition: Valence is a process profile of an emotion, mood, or affective bodily feeling (such as pleasure and pain). Valence can be positive or negative, with different strengths in both directions. For example, pleasure is positively valenced while pain is negatively valenced.
comment: A bodily process which brings into being, sustains or modifies a cognitive representation or a beahvior inducing state.
imported from: mfoem.owl

representation
type: Class
subclass of: specifically dependent continuant
definition: A dependent continuant which is about a portion of reality.
definition source: http://www.jbiomedsem.com/content/1/1/10
imported from: mfoem.owl

cognitive representation
type: Class
subclass of: specifically dependent continuant
subclass of: representation
definition: A representation which specifically depends on an anatomical structure in the cognitive system of an organism.
definition source: http://www.jbiomedsem.com/content/1/1/10
imported from: mfoem.owl

bodily disposition
type: Class
equivalent class: Restriction
  on property: inheres in at all times
  some values from: extended organism
subclass of: disposition
definition: A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language.
imported from: mfoem.owl

mental disposition
type: Class
subclass of: bodily disposition
subclass of: Restriction
  on property: realized in
  all values from: mental process
definition: A mental disposition is a bodily disposition that is realized in a mental process.
imported from: mfoem.owl

association
type: Class
subclass of: interaction
definition: Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
id: MI:0914
has_obo_namespace: PSI-MI
in_subset: PSI-MI slim
imported from: mi.owl
imported from: ino.owl

Mus musculus
type: Class
subclass of: Euarchontoglires
database_cross_reference: GC_ID:1
has_related_synonym: Mus muscaris
has_alternative_id: NCBITaxon:85055
has_exact_synonym: house mouse
has_related_synonym: mice C57BL/6xCBA/CaJ hybrid
has_exact_synonym: mouse
has_obo_namespace: ncbi_taxonomy
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

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

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

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
database_cross_reference: GC_ID:11
has_related_synonym: Monera
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11542017
database_cross_reference: PMID:11542087
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:270744
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: PMID:9336922
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
alternative term: eubacteria
has_exact_synonym: eubacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: not Bacteria Haeckel 1894
has_related_synonym: prokaryote
has_related_synonym: prokaryotes
has_rank: NCBITaxon superkingdom
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

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

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

Eukaryota
type: Class
subclass of: organism
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
editor preferred label: Eukaryota
has_related_synonym: Eukaryotae
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
alternative term: eucaryotes
has_exact_synonym: eucaryotes
has_related_synonym: eukaryotes
has_exact_synonym: eukaryotes
alternative term: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_rank: NCBITaxon superkingdom
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigation

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

Escherichia coli
type: Class
subclass of: Proteobacteria
has_related_synonym: Bacillus coli
has_related_synonym: Bacterium coli
has_related_synonym: Bacterium coli commune
has_exact_synonym: E. coli
has_related_synonym: Enterococcus coli
has_related_synonym: Escherchia coli
has_exact_synonym: Escherichia/Shigella coli
has_related_synonym: Eschericia coli
database_cross_reference: GC_ID:11
has_alternative_id: NCBITaxon:1637691
has_alternative_id: NCBITaxon:662101
has_alternative_id: NCBITaxon:662104
database_cross_reference: PMID:10319482
has_obo_namespace: ncbi_taxonomy
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Physarum polycephalum
type: Class
subclass of: Eukaryota
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
database_cross_reference: GC_ID:1
has_exact_synonym: human
has_exact_synonym: man
has_obo_namespace: ncbi_taxonomy
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

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

host role
type: Class
subclass of: role
definition source: 30 Mar09 submitted by vaccine community
editor note: 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
term editor: GROUP: Role Branch
example of usage: In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
definition source: OBI
editor preferred label: host role
definition: host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
definition source: http://en.wikipedia.org/wiki/Host_(biology)
has curation status: metadata complete
imported from: Ontology for Biomedical Investigation

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

infection process
type: Class
subclass of: pathologic process
subclass of: Restriction
  on property: has participant
  some values from: infection
subclass of: Restriction
  on property: realizes
  some values from: disposition to infect an organism
editor preferred label: infection process
definition source: IEDB
term editor: IEDB
definition: the detrimental process in which an infectious agent colonizes or replicates in a host environment
has curation status: metadata complete
imported from: Ontology for Biomedical Investigation

disposition to infect an organism
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized in
  all values from: infection process
editor preferred label: disposition to infect an organism
term editor: IEDB
definition source: IEDB
definition: Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
has curation status: metadata incomplete
imported from: Ontology for Biomedical Investigation

pathologic process
type: Class
subclass of: biological_process
editor preferred label: pathologic process
term editor: IEDB
definition source: IEDB
definition: abnormal, harmful processes caused by or associated with a disease
has curation status: metadata incomplete
imported from: Ontology for Biomedical Investigation

genome
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: gene
definition: A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
definition source: Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
term editor: Oliver He
definition source: WEB: http://en.wikipedia.org/wiki/Genome
imported from: ogg.owl

gene
type: Class
subclass of: material entity
subclass of: Restriction
  on property: transcribed to
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has disposition at all times
  some values from: gene disposition
definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
term editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
comment: In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.
imported from: ogg.owl

gene disposition
type: Class
subclass of: disposition
term editor: Yongqun He
definition: a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
definition source: WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
comment: YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition".
imported from: ogg.owl

phenotype
type: Class
subclass of: quality
curator notes: creation date: 2010-07-19T11:13:49Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
term editor: Albert Goldfain
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
imported from: ogms.owl

extended organism
type: Class
subclass of: material entity
term editor: Albert Goldfain
definition: An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
curator notes: creation date: 2010-01-25T04:51:11Z
definition source: http://code.google.com/p/ogms/issues/detail
imported from: ogms.owl

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

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

organ
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that performs a specific function or group of functions [WP].
external_ontology_notes: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
database_cross_reference: CARO:0020004
database_cross_reference: EFO:0000634
database_cross_reference: EMAPA:35949
database_cross_reference: ENVO:01000162
database_cross_reference: FMA:67498
database_cross_reference: MA:0003001
database_cross_reference: NCIT:C13018
database_cross_reference: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
database_cross_reference: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
external_definition: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
id: UBERON:0000062
database_cross_reference: UMLS:C0178784
database_cross_reference: WBbt:0003760
has_related_synonym: anatomical unit
has_related_synonym: body organ
has_related_synonym: element
has_obo_namespace: uberon
database_cross_reference: Organ (anatomy)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0178784
in_subset: upper level
imported from: uberon.owl
database_cross_reference: birnlex 4
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/272625005

organ part
type: Class
subclass of: multicellular anatomical structure
definition: A multicellular structure that is a part of an organ.
database_cross_reference: AAO:0011124
database_cross_reference: EFO:0000635
database_cross_reference: FMA:82472
id: UBERON:0000064
has_exact_synonym: cardinal organ part
curator notes: currently defined in a very broad sense, may be replaced by more specific classes in the future
has_related_synonym: regional part of organ
has_obo_namespace: uberon
in_subset: efo slim
in_subset: non informative
in_subset: upper level
imported from: uberon.owl
database_cross_reference: birnlex 16
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/113343008
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/91717005

tissue
type: Class
subclass of: multicellular anatomical structure
database_cross_reference: AAO:0000607
database_cross_reference: AAO:0010054
database_cross_reference: AEO:0000043
database_cross_reference: BILA:0000043
database_cross_reference: CALOHA:TS-2090
database_cross_reference: CARO:0000043
database_cross_reference: EHDAA2:0003043
database_cross_reference: EMAPA:35868
database_cross_reference: FBbt:00007003
database_cross_reference: FMA:9637
database_cross_reference: HAO:0000043
database_cross_reference: MA:0003002
database_cross_reference: MESH:D014024
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
database_cross_reference: NCIT:C12801
database_cross_reference: TAO:0001477
database_cross_reference: TGMA:0001844
id: UBERON:0000479
database_cross_reference: UMLS:C0040300
database_cross_reference: VHOG:0001757
database_cross_reference: WBbt:0005729
database_cross_reference: XAO:0003040
database_cross_reference: ZFA:0001477
editor note: changed label and definition to reflect CARO2
database_cross_reference: galen:Tissue
has_exact_synonym: portion of tissue
has_narrow_synonym: simple tissue
has_exact_synonym: tissue portion
has_obo_namespace: uberon
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0040300
in_subset: pheno slim
in_subset: upper level
imported from: uberon.owl
database_cross_reference: birnlex 19

anatomical entity
type: Class
subclass of: material entity
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BILA:0000000
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.
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: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
id: UBERON:0001062
database_cross_reference: UMLS:C1515976
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has_obo_namespace: uberon
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C1515976
in_subset: upper level
imported from: uberon.owl
database_cross_reference: birnlex 6

multicellular anatomical structure
type: Class
subclass of: anatomical entity
definition: An anatomical structure that has more than one cell as a part.
database_cross_reference: CARO:0010000
database_cross_reference: FBbt:00100313
id: UBERON:0010000
has_exact_synonym: multicellular structure
has_obo_namespace: uberon
in_subset: upper level
imported from: uberon.owl

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

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

ready for release
type: Thing
type: curation status specification
type: NamedIndividual
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."
has curation status: pending final vetting

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

pending final vetting
type: Thing
type: curation status specification
type: NamedIndividual
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
term editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
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.
term editor: Alan Ruttenberg
definition source: group:OBI
has curation status: pending final vetting

axiom holds for all times
type: NamedIndividual
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

Ontology for Biomedical Investigation
type: NamedIndividual
date: 2009-07-31
version info: 2017-11-07
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.
default language: en
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
subject: An ontology for the annotation of biomedical and functional genomics experiments.
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
Format: OWL-DL
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
description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
license: http://creativecommons.org/licenses/by/3.0/

bfo.owl
Contributor: Albert Goldfain
Contributor: Werner Ceusters
Contributor: Yongqun "Oliver" He
Contributor: Stefan Schulz
Contributor: Janna Hastings
Contributor: Robert Rovetto
Contributor: Melanie Courtot
Contributor: Randall Dipert
editor note: BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of one such primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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.
Contributor: Mauricio Almeida
Contributor: Bjoern Peters
Contributor: Fabian Neuhaus
Contributor: James A. Overton
Contributor: Larry Hunter
editor note: BFO 2 Reference: BFO’s treatment of continuants and occurrents – as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science [30
Contributor: Mathias Brochhausen
Contributor: David Osumi-Sutherland
Contributor: Pierre Grenon
Contributor: Mark Ressler
Contributor: Jie Zheng
Contributor: Leonard Jacuzzo
Contributor: Bill Duncan
editor note: BFO 2 Reference: BFO does not claim to be a complete coverage of all entities. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning – coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation [17
Contributor: Chris Mungall
Contributor: Thomas Bittner
Contributor: Barry Smith
Contributor: Jonathan Bona
Contributor: Ron Rudnicki
Contributor: Alan Ruttenberg
Contributor: Ludger Jansen
comment: The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1.
comment: This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif
license: http://creativecommons.org/licenses/by/3.0/

OBO Relations Ontology
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
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