Sustainability Core Ontology (SCO)
type: Ontology
version IRI: v1.1.0/sco-b
imports: bfo.owl
creator: Giorgio A. Ubbiali
description: SCO V1.1.0 aligns with two Top-Level Ontologies (TLOs), Basic Formal Ontology (BFO) and Unified Foundational Ontology (UFO). SCO V1.1.0 is comprised of two segments: SCO-B (B for BFO) and SCO-U (U for UFO). SCO-B aligns the SCO vocabulary with BFO (as SCO V1.0.0). SCO-U aligns the SCO vocabulary with gUFO (UFO implementation in the Web Ontology Language (OWL)). This file provides SCO-B segment. References – TLOs: https://github.com/BFO-ontology/BFO-2020 https://ontouml.readthedocs.io/en/latest/intro/ufo.html https://nemo-ufes.github.io/gufo/
description: SCO is a middle-level ontology, representing the major theoretical challenges to sustainability: 1) The polysemy of the term sustainability. 2) The relationship between sustainability and sustainable development. 3) The complexity underlying sustainability. SCO aims to play a pivotal role in harmonizing and integrating top-level and domain ontologies regarding sustainability.
license: https://creativecommons.org/licenses/by/4.0/
title: L'ontologia fondazionale della sostenibilità @it
title: L'ontologie fondationnelle de la durabilité @fr
see also: Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
prior version: SCO V1.0.1. constitutes the prior version of this resources. SCO V1.0.1. is available on GitHub at the following link: https://github.com/gioUbbiali/Sustainability-Core-Ontology/releases/tag/v1.0.1-revisions
version info: 2025-03-19
version info: Version 1.1.0. ; segment B.
note: Currently, this resource includes labels and definitions in the following three natural languages: English, Italian, and French. In the next version of this resource, the creator intends to also encompass Italian and French translations of the remaining pieces of information as well as to cover other natural languages.
note: Repository: https://github.com/gioUbbiali/Sustainability-Core-Ontology Documentation webpage: https://www.w3id.org/sco/docs
note: The current version of SCO does not cover classes and object properties accounting for systems granularity, scales, and levels. A deeper representation of system change and behaviors is equally required. These themes will be topics of inclusion in the next version of this resource.
note: The current version of this resource does not include semi-formal natural language definitions or First Order Logics definitions. In the next version of this resource, the creator intends to also include them.
note: The most recent version of this file is available on GitHub at the following link: https://www.w3id.org/sco

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

contributor
type: AnnotationProperty
definition: entity responsible for making contributions to the resource

creator
type: AnnotationProperty
definition: entity responsible for making the resource
sub property of: contributor

source
type: AnnotationProperty
definition: related resource from which the described resource is derived
explanatory note: The intent is to provide a user with a reference as to how the thing being annotated was derived or arrived at. - The source can be a URL to a standard, common dictionary (e.g. Oxford), or similar reference. Or it can be a short description of where the entity being annotated was derived from. - The 'Source' annotation would most likely be used as an annotation on an annotation. For instance annotating a Natural Language definition annotation.

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

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

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

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

adapted from
type: AnnotationProperty
definition: source for the resource that was modified to create the subject resource
sub property of: source

direct source
type: AnnotationProperty
definition: definitive source of the subject resource
sub property of: source

excerpted from
type: AnnotationProperty
definition: source of a resource that was imported unmodified from an external ontology
usage note: This annotation is to be used when an element from a non-IOF ontology is used in an IOF ontology (and the source ontology is not imported in its entirety).
sub property of: source

explanatory note
type: AnnotationProperty
definition: note that provides additional explanatory information about a given notion or resource
sub property of: note

first-order logic axiom
type: AnnotationProperty
definition: logic axiom annotation written in first order logic
usage note: First-order logic axioms MAY be provided if the term is primitive ('is primitive' is true ) or non-primitive. A construct MAY include more than one first-order logic axiom annotation.
sub property of: logic axiom

first order logic definition
type: AnnotationProperty
definition: logic definition that expresses the axioms of a class or an object property in first order logic
example: An example of a First Order Logic definition for 'Product' might be (again bearing in mind the natural language terms appearing should be regarded as symbols in the IOF signature): - Continuant(x) ∧ ¬(SpecificallyDependentContinuant(x) ∨ Person(x) ∨ Organization(x)) ∧ ∃r (ProductRole(r) ∧ hasRole(x, r))
usage note: The First Order Logic Definition annotation is comprised of the (complete) necessary and sufficient conditions. - This annotation is Required for each non-primitive (aka non-axiomatic) class (i.e. unary relation) of a published IOF OWL ontology. This is the most authoritative and comprehensive definition of an IOF element. - IOF Common Logic ontologies do not require this annotation, but if included it must be logically equivalent to the Common Logic definition. - A primitive (aka axiomatic) term will not have a First Order Logic definition in either an OWL or Common Logic IOF ontology. - There should be at most one First Order Logic definition. - The specific symbols to be used for existential and universal quantification along with those for conjunction, disjunction, negation, conditional (i.e. if-then), and equivalence will be those commonly used in the mathematical formulas and statement. - Conjunction - ∧; Disjunction - ∨; Negation - ¬; Existential Quantification - ∃; Universal Quantification - ∀; Conditional - →; Equivalence - ↔; Left/Right Parentheses - (,); Left/Right Brackets - {,}.
sub property of: logic definition

is primitive
type: AnnotationProperty
definition: boolean flag indicating that necessary and sufficient conditions are not provided
usage note: 'is primitive' must be present if the term does not have necessary and sufficient conditions and the value of the annotation must be set to true. When 'is primitive' is set to true, a value for a 'primitive rationale' annotation must also be provided.

logic axiom
type: AnnotationProperty
definition: logical statements constraining the interpretation of the notion represented by the construct that do not provide necessary and sufficient conditions
explanatory note: This annotation property is an abstraction of the more specialized logic axiom annotations used in IOF. However, this annotation property can also be used to group together the logic axiom annotation values of different forms (such as FOL and natural language) that express the same meaning for a particular construct.
usage note: A first order logic axiom expression and a semi-formal natural language axiom expression should be added as Property values for each logic axiom annotation using 1 of each of the corresponding logic axiom annotation subproperties.
sub property of: note

logic definition
type: AnnotationProperty
definition: definition in the form of a logical expression
sub property of: definition

maturity
type: AnnotationProperty
definition: annotation property used to indicate the development status of a resource
usage note: Any value for maturity MUST be an instance of MaturityLevel. All IOF ontologies MUST include exactly one maturity annotation. IOF constructs may include a maturity annotation.

natural language definition
type: AnnotationProperty
definition: definition written in plain text for human understanding
usage note: This annotation is Required for each non-primitive or non-axiomatic class of an IOF (OWL or Common Logic) ontology. - It is optional for primitive (aka axiomatic) classes since such the Elucidation annotation is required and will satisfy the role of a natural language definition. - It is optional, but recommended, for relations when the intent of a relation may be misunderstood. - There should be at most one. - This natural language definition should be subject matter expert friendly and consistent with any formal definition or elucidation. - Natural language definitions should use class and relation names with following caveats: a) Relations – For those relations whose label (i.e. local identifier) consist of multiple terms hyphenate the terms of the label: e.g. 'hasPlan' would be written as 'has-plan' b) Classes – For classes whose label has multiple distinct terms, e.g, ManufacturingOperationSpecification, separate the terms but bound them with apostrophe marks: 'Manufacturing Operation Specification'.
sub property of: definition

primitive rationale
type: AnnotationProperty
definition: reason why necessary and sufficient conditions could not be provided
usage note: When 'is primitive' is set to true, a value for 'primitive rationale' must be provided. The rationale should indicate what is missing if additional work is required to define necessary and sufficient conditions.
sub property of: note

semi-formal natural language axiom
type: AnnotationProperty
definition: logic axiom expressed in natural language
usage note: Semi-formal natural language axioms MAY be provided if the term is primitive (is primitive is true). A construct MAY include more than one semi-formal natural language axiom annotation.
sub property of: logic axiom

semi-formal natural language definition
type: AnnotationProperty
definition: logic definition that expresses a first order logic definition or common logic definition in natural language
usage note: This annotation is required if an element in an IOF OWL ontology has a First Order Logic definition or in a IOF Common Logic (where the element is defined using Common Logic). - The intent of this annotation to provide a transition or bridge from the First Order Logic definition of a notion to the natural language definition. This definition is intended to help a user understand the intended interpretation of the notion. - As example using the First Order Logic definition of 'Product' above, a semi-formal translation of that might be: - Product =def. Continuant that is not a Person and not an Organization and not a Specifically Dependent Continuant and there is a Product Role that the thing has or bears.
sub property of: logic definition

subject matter expert explanation
type: AnnotationProperty
definition: definition of the term expressed in natural language that has the minimal usage of ontological terms and is intended to be a self-standing explanation
usage note: Usage of this annotation is optional but is recommended in cases where: - the natural language definition or elucidation rely heavily on the terms defined in the ontology - there exists an explanation of the term that is more familiar to SMEs that does not coincide with the definition present in the ontology
sub property of: definition

usage note
type: AnnotationProperty
definition: note that provides information about how a given notion or resource is used in the ontology's context
sub property of: note

according to the perspective
type: AnnotationProperty
comment: We envisage using this annotation property to highlight (indirectly) the grounding of certain entities on perspectives and characterize them according to the embraced perspective(s). Here, it is provided an explicative example. Let’s consider that two users, A and B, endorse two different perspectives on sustainability, perspective A and perspective B. These perspectives lead to considering different complex system components as stakeholders of the complex system of interest. (This is an explicative example. It could also be the case that there is just one single user who wants to characterize the same entity according to two perspectives on sustainability, or who wants to provide an additional characterization according to a different perspective than the one previously covered.) We suggest proceeding as follows. First, the class “perspective” can be instantiated with two “perspective” individuals, “perspective A” and “perspective B”. These “perspective” individuals will provide descriptions and other relevant information regarding users’ perspectives. Then, two subclasses, “stakeholder – A” and “stakeholder – B”, can be added to the class “stakeholder”. These classes could be created manually and further populated with further subclasses and/or individuals. Alternatively, they can be created by adding SPARQL query results to the ontology, directly as classes or as classes equivalent to some new classes manually created. Subclasses “stakeholder – A” and “stakeholder – B” will cover stakeholders according to the two different user perspectives. Finally, this annotation property can be used to annotate these two subclasses with the corresponding individual “perspective A” and “perspective B”. In proceeding as such, we can highlight the grounding of the role of stakeholder (entity) on perspective (entity) and provide stakeholder characterizations according to the two user perspectives. This procedure supports establishing indirectly the grounding of certain entities o…
label: secondo la prospettiva @it
label: selon la perspective @fr
range: sco.owl/SCO 0000016

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

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: BFO_0000020
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
textual definition: Inverse of characteristic_of
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative label: bearer_of
alternative label: is bearer of

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: BFO_0000034
example of usage: this catalysis function is a function of this enzyme
textual definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative label: function_of
alternative label: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

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

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

has function
type: ObjectProperty
sub property of: has characteristic
domain: BFO_0000004
range: BFO_0000034
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
textual definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative label: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: BFO_0000019
example of usage: this apple has quality this red color
textual definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: BFO_0000004
range: BFO_0000023
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
textual definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative label: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: BFO_0000004
range: BFO_0000016
textual definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
textual definition: inverse of has disposition
in subset: RO_0002259
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
has curation status: IAO_0000125
textual definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
temporal interpretation: RO_0001901
in subset: ro-eco

characteristic of part of
type: ObjectProperty
sub property of: depends on
textual definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

mereotopologically related to
type: ObjectProperty
textual definition: A mereological relationship or a topological relationship
term editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
temporal interpretation: RO_0001901

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

is about
type: ObjectProperty
inverse of: is subject of
domain: Information Content Entity
range: BFO_0000001
definition: A primitive relationship between an Information Content Entity and some Entity.
definition source: http://purl.obolibrary.org/obo/IAO_0000136
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology

is subject of
type: ObjectProperty
range: Information Content Entity
definition: A primitive relationship between an instance of an Entity and an instance of an Information Content Entity.
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology

represented by
type: ObjectProperty
sub property of: is subject of
inverse of: represents
range: Representational Information Content Entity
definition: y represented_by x iff x is an instance of Information Content Entity, and y is an instance of Entity, and z is carrier of x, such that x is about y in virtue of there existing an isomorphism between characteristics of z and y.
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
comment: See notes for inverse property.

represents
type: ObjectProperty
sub property of: is about
domain: Representational Information Content Entity
definition: x represents y iff x is an instance of Information Content Entity, y is an instance of Entity, and z is carrier of x, such that x is about y in virtue of there existing an isomorphism between characteristics of z and y.
elucidation: The relationship that is being defined here is that between the content of a photographic image and its object, between the content of a video and its objects and events, between the content of an audio recording and the sounds or events generating those sounds, or between the content of a written transcript and the verbal event that it transcribes.
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
comment: Isomorphism between the carrier of x and the represented entity can be via a direct similarity relation, e.g., grooves in a vinyl record corresponding to sound waves, or linguistic convention, e.g., a court stenographer's transcription of spoken words, as well as others, such as encoding processes for images.
scope note: Given a stronger temporal interpretation, this property may be functional. For more info please refer to https://github.com/BFO-ontology/BFO-2020/tree/master/src/owl/temporal%20extensions.

has agent at time t
type: ObjectProperty
sub property of: BFO_0000057
inverse of: agent in at time t
domain: BFO_0000015
range: Class
  union of: BFO_0000020
  union of: BFO_0000031
  union of: Class
    intersection of: BFO_0000004
    intersection of: Class
      complement of: BFO_0000006
comment: We envision revisions of the current SCO theory of agency. This is due to the limited power of explainability of present representation. A sounder and deeper interpretation of the causal role of an agent in an interaction, compared to other participants, is required. Tentative proposal: a possible direction of implementation is towards a telic vision of agency intended as end-point driven. On this more fundamental neutral vision, a second layer of representation may be constructed to model intentionality, goals, and plans in relation to agency. Here, SCO may harmonize and align with UFO-C representation. For insight for discussion see: Guarino, N., & Guizzardi, G. (2024). Processes as variable embodiments. Synthese, 203(4), 104. https://doi.org/10.1007/s11229-024-04505-2 Guizzardi, G., de Almeida Falbo, R., & Guizzardi, R. (2008). Grounding software domain ontologies in the unified foundational ontology (UFO): The case of the ODE. Memorias de la XI Conferencia Iberoamericana de Software Engineering (CIbSE 2008), Recife, Pernambuco, Brasil, February 13-17, 2008, 127–140.
comment: Common Core Ontologies (CC) provide corresponding properties for this and the “agent at time t” relations. See “see also” annotation”. As these relations apply specifically to the CCO “Agent” class and lack reference to time, the SCO creator decided to establish SCO's own versions of these relations, directly referring to the original source. See “adapted from” annotation.
comment: Future implementations may involve the introduction of an “act within the system” class, to deepen the characterization of system agency. Insights to implementation may come from the following CCO classes: http://www.ontologyrepository.com/CommonCoreOntologies/Act http://www.ontologyrepository.com/CommonCoreOntologies/IntentionalAct http://www.ontologyrepository.com/CommonCoreOntologies/Agent http://www.ontologyrepository.com/CommonCoreOntologies/AgentCapability The aim is to align SCO and CCO “agent” classes in order to have a shared theory of agency.
label: a un agent au temps t @fr
label: ha un agente al tempo t @it
see also: comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029
definition: A primitive relation between a process x, a continuant y, and a time at which y is causally active in x.
definition: Una relazione primitiva tra un processo x, un continuante y e un tempo t a cui y è causalmente attivo in x. @it
definition: Une relation primitive entre un processus x, un continuant y et un temps t auquel y est causalement actif en x. @fr
adapted from: https://doi.org/10.1186/gb-2005-6-5-r46
maturity: provisional

agent in at time t
type: ObjectProperty
sub property of: BFO_0000056
domain: Class
  union of: BFO_0000020
  union of: BFO_0000031
  union of: Class
    intersection of: BFO_0000004
    intersection of: Class
      complement of: BFO_0000006
range: BFO_0000015
comment: We envision revisions of the current SCO theory of agency. This is due to the limited power of explainability of present representation. A sounder and deeper interpretation of the causal role of an agent in an interaction, compared to other participants, is required. Tentative proposal: a possible direction of implementation is towards a telic vision of agency intended as end-point driven. On this more fundamental neutral vision, a second layer of representation may be constructed to model intentionality, goals, and plans in relation to agency. Here, SCO may harmonize and align with UFO-C representation. For insight for discussion see: Guarino, N., & Guizzardi, G. (2024). Processes as variable embodiments. Synthese, 203(4), 104. https://doi.org/10.1007/s11229-024-04505-2 Guizzardi, G., de Almeida Falbo, R., & Guizzardi, R. (2008). Grounding software domain ontologies in the unified foundational ontology (UFO): The case of the ODE. Memorias de la XI Conferencia Iberoamericana de Software Engineering (CIbSE 2008), Recife, Pernambuco, Brasil, February 13-17, 2008, 127–140.
label: agent en au temps t @fr
label: agente in al tempo t @it
see also: comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029
see also: See information under the inverse "has agent at t" property.
definition: A primitive relation between a continuant x, a process y, and a time at which x is causally active in y.
definition: Una relazione primitiva tra un continuante x, un processo y e un tempo t a cui x è causalmente attivo in y. @it
definition: Une relation primitive entre un continuant x, un processus y et un temps t auquel x est causalement actif en y. @fr
maturity: provisional

BFO_0000004
textual definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])

BFO_0000015
textual definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])

BFO_0000020
textual definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])

BFO_0000023
textual definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.

BFO_0000031
textual definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])

BFO_0000040
textual definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

system
type: Class
subclass of: BFO_0000040
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000110
    some values from: BFO_0000040
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000110
    some values from: system component
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000111
    some values from: system boundary
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000166
    some values from: system development
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000185
    some values from: system history
  intersection of: Restriction
    on property: BFO_0000185
    all values from: system history
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000211
    some values from: system spatial region
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: spatially disjoint from
    some values from: system environment
disjoint with: system environment
textual definition: A material entity consisting of multiple components that are causally integrated.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.jbiomedsem.com/content/4/1/43
comment: SCO cretor comment: RO defines the class “system” as a subclass of the “material entity” class. Nevertheless, a system is a fiat object, e.g. an object that is “delimited” according to the perspective of the stakeholder (Landgrebe and Smith 2022, p. 117,118). System delimitation determines the boundaries of the systems, but the stakeholder, however, does not create the system through this delimitation process (Landgrebe and Smith 2022, p. 117,118). As this class is extensively reused among ontologies within the OBO-Foundry context, we maintain its current hierarchical position. However, we recommend a revision of this class. There are two possible strategies to consider: 1) to reclassify this class as a subclass of “fiat object part” one or 2) to create a dedicated “fiat object” class that will be a subclass of “material entity” and the superclass for the “system” one (and related subclasses). We leave the discussion open with the intention of engaging with subject matter experts, planning that these modifications may be included in the next release of this resource. As the environment of a system corresponds to what has not been delimited as part of such a system, these considerations correspondingly also apply to the class “system environment” (at least regarding the system-system environment boundaries).
comment: SCO developer comment: Despite minor differences, SCO representation of systems and related architecture and composition is compatible with that of the System Core Ontology (Calhau et al., 2024). The system Core Ontology centers on socio-techno systems, primarily pointing to an intention/goal-directed representation of these systems. SCO representation, instead, adopts a more neutral modeling approach for complex systems, seeking to account for a wider range of systems. SCO is also more compact than the system Core Ontology. This is, however, adequate for the current purposes of SCO. We envision employing the system Core Ontology as a starting point to extend SCO representation of system architecture, situations, properties, and functions. We also envision possible alignments and reciprocal implementations between these two ontologies. Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
comment: SCO developer comment: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
see also: SCO creator cited reference: Landgrebe, Jobst, and Barry Smith. 2022. Why Machines Will Never Rule the World: Artificial Intelligence without Fear. Taylor & Francis. 10.4324/9781003310105

Axiom
annotated source: system
annotated property: comment
annotated target: SCO developer comment: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
see also: See also comments to https://www.w3id.org/sco/sco-u#SCO_0000056

Information Content Entity
type: Class
equivalent class: Class
  intersection of: BFO_0000031
  intersection of: Restriction
    on property: is about
    some values from: BFO_0000001
subclass of: BFO_0000031
alternative label: ICE
definition: A Generically Dependent Continuant that generically depends on some Information Bearing Entity and stands in relation of aboutness to some Entity.
definition source: http://purl.obolibrary.org/obo/IAO_0000030
elucidation: Information Content Entity is here intended to be a class of Entities whose instances are the informational content of Information Bearing Entities. For example, three instances of information bearers -- such as a bar chart, color-coded map, and a written report -- each of which lists the GDP of Countries for the year 2010 are each different carriers of the same information content. It is this content that is generically dependent upon its carrier. This treatment of Informational Content Entity (cf. the Information Artifact Ontology) leads to a principle of subtyping based upon the relationship that ICE's have with the Entity they are about rather than characteristics such as format, language, measurement scale, or media. The latter are treated here as being Qualities of bearers.
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology
comment: SCO developer comment: Currently, SCO-B reuses the representation of information that belongs to IAO/CCO. Nevertheless, debates are ongoing on whether information may be better represented through a type-token relationship within a multi-level type hierarchy. See the paper cited at the end of the comment. We envision discussions with subject matter experts from both BFO and UFO communities regarding this point. Weigand, H. (2025). Generic Ontological Dependence⋆. https://www.utwente.nl/en/eemcs/vmbo2025/papers/vmbo-2025-paper-4-2.pdf
comment: SCO developer comment: SCO-B does not currently cover a class for information bearing entity. We directly refer ICE subclasses to corresponding information bearing entities.

Representational Information Content Entity
type: Class
equivalent class: Class
  intersection of: Information Content Entity
  intersection of: Restriction
    on property: represents
    some values from: BFO_0000001
subclass of: Information Content Entity
disjoint with: perspective information content entity
disjoint with: worth information content entity
definition: An Information Content Entity that represents some Entity.
example of usage: the content of a court transcript represents a courtroom proceeding
example of usage: the content of a photograph of the Statue of Liberty represents the Statue of Liberty
example of usage: the content of a video of a sporting event represents that sporting event
is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology

maturity level
type: Class
definition: classifier used to specify the state of a resource in its development process

interaction
type: Class
equivalent class: Class
subclass of: BFO_0000015
subclass of: Class
  intersection of: BFO_0000015
  intersection of: Restriction
    on property: has agent at time t
    some values from: Class
      intersection of: BFO_0000004
      intersection of: Class
        complement of: BFO_0000006
subclass of: Class
  intersection of: BFO_0000015
  intersection of: Restriction
    on property: BFO_0000167
    min qualified cardinality: 2
    on class: Class
      intersection of: BFO_0000004
      intersection of: Class
        complement of: BFO_0000006
comment: In the original definition, INO developers define this class with respect to interactors involved in the interaction process. INO includes the classes “interactor” and “interactor role” (see SeeAlso note). Here, we generalize this definition, excluding reference to interactors. In the context of SCO, we aim to provide users with an upper-level class that generally points to the involvement of material entities in an interaction process mutually influencing each other. We suggest not using this class directly but, instead, extending SCO-provided subclasses as needed. We wish users to classify interactions according to whether they occur among system components, among system environment components, or between system and system environment components. Original definition: “Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.”
label: interazione @it
definition: A process that has at least two independent continuants (no spatial regions) as participants that have an effect upon one another.
definition: Un processo che ha almeno due continuanti indipendenti (no regioni spaziali) come partecipanti, aventi un effetto l’una sull’altra. @it
definition: Un processus qui a au moins deux continuants indépendants (pas de régions spatiales) comme participants, ayant un effet l’une sur l’autre. @fr
adapted from: http://purl.obolibrary.org/obo/INO_0000002
maturity: released

Axiom
annotated source: interaction
annotated property: equivalentClass
annotated target: Class
comment: This class has been restricted to those specific subclasses for the purposes of SCO.

system development
type: Class
subclass of: BFO_0000015
subclass of: Class
  intersection of: BFO_0000015
  intersection of: Restriction
    on property: BFO_0000167
    some values from: system
disjoint with: system history
comment: SCO must extend its representation to (complex) system behaviors. A possible starting point may be the work of Calhau et al. (2023) and Calhau et al. (2024). Calhau, R., Sales, T. P., Almeida, J. P. A., & Guizzardi, G. (2023). Exploring system behavior in a system ontology. Int Conf Concept Model. Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1
comment: This class aims to be the starting point for developing a representation of system change. Future SCO implementations will provide additional classes and object properties addressing system behaviors, system processes, system scales and levels, and related themes. Related axioms must be revised accordingly.
label: développement de système @fr
label: sviluppo del sistema @it
definition: A process whose specific outcome is the progression of a system over time from an initial condition to a later condition.
definition: Un processo il cui specifico risultato è la progressione di un sistema nel tempo da una condizione iniziale a una condizione successiva. @it
definition: Un processus dont le résultat spécifique est la progression d’un système dans le temps, depuis une condition initiale à une condition suivante. @fr
adapted from: http://purl.obolibrary.org/obo/GO_0032502
maturity: provisional

indicator value
type: Class
equivalent class: Class
subclass of: Representational Information Content Entity
subclass of: Class
  intersection of: Representational Information Content Entity
  intersection of: Restriction
    on property: BFO_0000084
    some values from: indicator
has_related_synonym: indicator information
label: il valore dell'indicatore @it
label: la valeur de l’indicateur @fr
see also: See the comments under the corresponding "indicator" class.
definition: A representational information content entity that generically depends on some indicator and is about, providing insights into, the complex system to which the indicator belongs.
definition: Un contenu représentatif d’information qui dépend de façon générique d’un indicateur et qui concerne, fournissant des indications/renseignements, sur le système complexe auquel l’indicateur appartient. @fr
definition: Un contenuto informativo rappresentativo che genericamente dipende da un indicatore e riguarda, fornisce informazioni sul, sistema complesso a cui l'indicatore appartiene. @it
maturity: provisional

Axiom
annotated source: indicator value
annotated property: equivalentClass
annotated target: Class
comment: Discussion with subject matter experts is required to revise this axiom with regard to the “represents” object property. This was the most appropriate object property among those pertaining to OBO-Foundry and compliant ontologies to use in constructing this axiom. Nevertheless, implementations seem necessary to deepen the characterization, for instance with regard to representing and measuring the complex system of interest.. Revisions may regard adapting this object property or even further creating a new ad hoc object property. The CCO object properties “describes” and “is measurement of” appear other interesting options. http://www.ontologyrepository.com/CommonCoreOntologies/describes http://www.ontologyrepository.com/CommonCoreOntologies/is_a_measurement_of

perspective information content entity
type: Class
equivalent class: Class
  intersection of: Information Content Entity
  intersection of: Restriction
    on property: is about
    some values from: perspective
subclass of: Information Content Entity
subclass of: Class
  intersection of: Information Content Entity
  intersection of: Restriction
    on property: BFO_0000084
    some values from: Class
      union of: complex system environment component
      union of: complex system component
subclass of: Class
  intersection of: Information Content Entity
  intersection of: Restriction
    on property: BFO_0000165
    some values from: perspective
disjoint with: worth information content entity
label: contenu informatif de la perspective @fr
label: contenuto informativo della prospettiva @it
definition: An information content entity that generically depends on some complex system component or complex system environment component and is about the perspective (that concretizes it) of that complex system component or complex system environment component.
definition: Un contenu d’information qui dépend de façon générique d’une composante de système complexe ou d’une composant d’environnement de système complexe et qui concerne la perspective (qui le concrétise) de cette composante de système complexe ou de cette composante environnement de système complexe. @fr
definition: Un contenuto informativo che dipende genericamente da una componente del sistema complesso o da una componente dell'ambiente del sistema complesso e riguarda la prospettiva (che lo concretizza) di tale componente del sistema complesso o dell’ambiente del sistema complesso. @it
maturity: released

worth information content entity
type: Class
equivalent class: Class
  intersection of: Information Content Entity
  intersection of: Restriction
    on property: is about
    some values from: worth-role
subclass of: Information Content Entity
subclass of: Class
subclass of: Class
  intersection of: Information Content Entity
  intersection of: Restriction
    on property: BFO_0000165
    some values from: worth-role
label: contenu informatif de la valeur @fr
label: contenuto informativo del valore @it
definition: An information content entity that generically depends on a complex system or a complex system environment (or some part(s) of them) and is about the worth (that concretizes it) that some complex system component or complex system environment component recognizes that that complex system or complex system environment (or some part(s) of them) bearer.
definition: Un contenu d’information qui dépend de façon générique d’un système complexe ou de l’environnement de système complexe (ou une ou plus parties de ceux-ci) et qui concerne la valeur (qui le concrétise) qu’une composante de système complexe ou de son environnement reconnaît d’avoir à ce système complexe-là ou à ce-t-environnement de système complexe-là (ou une ou plus parties de celux-ci). @fr
definition: Un contenuto informativo che dipende genericamente dal sistema complesso o dall'ambiente del sistema complesso (o una o più parti di essi) e riguarda il valore (che lo concretizza) che una componente del sistema complesso del suo ambiente riconosce di avere a quel sistema complesso o ambiente del sistema complesso (o una o più parti di essi). @it
maturity: released

Axiom
annotated source: worth information content entity
annotated property: subClassOf
annotated target: Class
comment: To amend this axiom in case worth is associated with some object aggregate that is part of the complex system or complex system environment of interest. To extend this axiom to also cover the "object aggregate" class.

system environment
type: Class
subclass of: BFO_0000040
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000110
    some values from: BFO_0000040
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000110
    some values from: system environment component
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: spatially disjoint from
    some values from: system
has_exact_synonym: system context
comment: See the comment under the "system" class.
comment: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
label: ambiente del sistema @it
label: environnement de système @fr
definition: A material entity that surrounds and is distinct and disjoint from a system.
definition: Un'entità materiale che circonda ed è distinta e disgiunta da un sistema. @it
definition: Une entité matérielle qui entourne et qui est distincte et disjointe d’un système. @fr
maturity: provisional

Axiom
annotated source: system environment
annotated property: comment
annotated target: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
see also: See also comments to https://www.w3id.org/sco/sco-u#SCO_0000056

interaction among system components
type: Class
subclass of: interaction
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has agent at time t
    some values from: system agent
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has agent at time t
    all values from: system agent
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: BFO_0000167
    min qualified cardinality: 2
    on class: system component
disjoint with: interaction among system environment components
disjoint with: interaction between system components and system environment components
has_related_synonym: relation among system components, interconnection among system components
label: Interaction entre les composantes de système @fr
label: interazione tra le componenti del sistema @it
definition: An interaction that occurs among at least two system components.
definition: Une interaction qui se produit entre au moins deux composantes de système. @fr
definition: Un’interazione che avviene tra almeno due componenti del sistema. @it
maturity: released

interaction among system environment components
type: Class
subclass of: interaction
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has agent at time t
    some values from: system environnement agent
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has agent at time t
    all values from: system environnement agent
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: BFO_0000167
    min qualified cardinality: 2
    on class: system environment component
disjoint with: interaction between system components and system environment components
has_related_synonym: relation among system environment components, interconnection among system environment components
label: interaction entre les composantes de l’environnement de système @fr
label: interazione tra le componenti dell’ambiente di sistema @it
definition: An interaction that occurs among at least two system environment components.
definition: Une interaction qui se produit entre au moins deux composantes de l’environnement d’un système. @fr
definition: Un’interazione che avviene tra almeno due componenti dell’ambiente di un sistema. @it
maturity: released

interaction between system components and system environment components
type: Class
subclass of: interaction
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: BFO_0000167
    some values from: system component
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: BFO_0000167
    some values from: system environment component
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has agent at time t
    some values from: Class
      union of: system environnement agent
      union of: system agent
subclass of: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has agent at time t
    all values from: Class
      union of: system environnement agent
      union of: system agent
has_related_synonym: relation between system components and the system environment, interconnection between system components and the system environment
label: Interaction entre les composantes de système et les composantes de l’environnement de système @fr
label: interazione tra le componenti del sistema e le componenti de l'ambiente del sistema @it
definition: An interaction that occurs between at least one system component and one system environment component where the latter belongs to the system environment of the system to which the system component belongs.
definition: Une interaction qui se produit entre au moins une composante d’un système et au moins une composante de l’environnement du système auquel la composante de système appartient. @fr
definition: Un’interazione che avviene tra almeno una componente di un sistema e almeno un componente dell’ ambiente del sistema a cui la componente del sistema appartiene. @it
maturity: released

complex system development
type: Class
subclass of: system development
subclass of: Class
  intersection of: system development
  intersection of: Restriction
    on property: BFO_0000167
    some values from: complex system
disjoint with: complex system history
label: développement de système complexe @fr
label: sviluppo del sistema complesso @it
definition: Le développement d’un système complexe. @fr
definition: Lo sviluppo di un sistema complesso. @it
definition: The system development of a complex system.
maturity: provisional

system history
type: Class
equivalent class: Class
  intersection of: BFO_0000182
  intersection of: Restriction
    on property: BFO_0000184
    some values from: system
  intersection of: Restriction
    on property: BFO_0000184
    all values from: system
subclass of: BFO_0000182
label: historie de système @fr
label: storia del sistema @it
definition: La storia di un sistema. @it
definition: L’histoire d’un système. @fr
definition: The history of a system.
maturity: released

complex system environment
type: Class
subclass of: system environment
subclass of: Class
  intersection of: system environment
  intersection of: Restriction
    on property: BFO_0000110
    some values from: complex system environment component
subclass of: Class
  intersection of: system environment
  intersection of: Restriction
    on property: spatially disjoint from
    some values from: complex system
disjoint with: complex system
has_exact_synonym: complex system context
label: ambiente del sistema complesso @it
label: environnement de système complexe @fr
definition: A system environment that surrounds and is distinct and disjoint from a complex system.
definition: Un ambiente del sistema che circonda ed è distinto e disgiunto da un sistema complesso. @it
definition: Un environnement de système qui entourne et qui est distinct et disjoint d’un système complexe. @fr
maturity: provisional

system component
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000176
    some values from: system
subclass of: BFO_0000040
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Class
    complement of: system environment component
disjoint with: system environment component
has_exact_synonym: system element
has_related_synonym: system variable
comment: Despite minor differences, SCO representation of systems and related architecture and composition is compatible with that of the System Core Ontology (Calhau et al., 2024). The system Core Ontology centers on socio-techno systems, primarily pointing to an intention/goal-directed representation of these systems. SCO representation, instead, adopts a more neutral modeling approach for complex systems, seeking to account for a wider range of systems. SCO is also more compact than the system Core Ontology. This is, however, adequate for the current purposes of SCO. We envision employing the system Core Ontology as a starting point to extend SCO representation of system architecture, situations, properties, and functions. We also envision possible alignments and reciprocal implementations between these two ontologies. Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
comment: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
label: componente del sistema @it
label: composante de système @fr
definition: A material entity that belongs to a system.
definition: Un'entità materiale che appartiene a un sistema. @it
definition: Une entité matérielle qui appartient à un système. @fr
maturity: released

Axiom
annotated source: system component
annotated property: comment
annotated target: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
see also: See also comments to https://www.w3id.org/sco/sco-u#SCO_0000056

system environment component
type: Class
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: BFO_0000176
    some values from: system environment
subclass of: BFO_0000040
subclass of: Class
  intersection of: BFO_0000040
  intersection of: Class
    complement of: system component
has_exact_synonym: system environment element
has_related_synonym: system environment variable
comment: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
label: componente dell' ambiente del systema @it
label: composante de l'environnement de système @fr
definition: A material entity that belongs to a system environment.
definition: Un'entità materiale che appartiene all’ambiente di un sistema. @it
definition: Une entité matérielle qui appartient à l’environnement d’un système. @fr
maturity: released

Axiom
annotated source: system environment component
annotated property: comment
annotated target: We envision discussions with subject matter experts regarding whether the current SCO representation of system-system component (and related environment) parthood is suitable or whether a proper parthood-based representation is more adequate. Insights for discussion may be found in Calhau et al. (2024) and Ubbiali et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
see also: See also comments to https://www.w3id.org/sco/sco-u#SCO_0000056

complex system
type: Class
equivalent class: Class
  intersection of: system
  intersection of: Restriction
    on property: has quality
    some values from: Class
      union of: emergence
      union of: self-organization
subclass of: system
subclass of: Class
  intersection of: system
  intersection of: Restriction
    on property: BFO_0000110
    some values from: complex system component
subclass of: Class
  intersection of: system
  intersection of: Restriction
    on property: BFO_0000111
    some values from: complex system boundary
subclass of: Class
  intersection of: system
  intersection of: Restriction
    on property: BFO_0000166
    some values from: complex system development
subclass of: Class
  intersection of: system
  intersection of: Restriction
    on property: BFO_0000185
    some values from: complex system history
  intersection of: Restriction
    on property: BFO_0000185
    all values from: complex system history
subclass of: Class
  intersection of: system
  intersection of: Restriction
    on property: BFO_0000211
    some values from: complex system spatial region
subclass of: Class
  intersection of: system
  intersection of: Restriction
    on property: spatially disjoint from
    some values from: complex system environment
definition source: Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr
has_narrow_synonym: socio-ecological system, social-ecological system
label: sistema complesso @it
label: système complexe @fr
see also: IOBC: http://purl.jp/bio/4/id/200906033993517889 IOBC: http://purl.jp/bio/4/id/201406059151625127 EnvThes: http://vocabs.lter-europe.net/EnvThes/21908 I2SV: https://i2insights.org/index/integration-and-implementation-sciences-vocabulary#complex-systems
definition: A system whose system components interact dynamically and nonlinearly, causing the emergence of a collective nontrivial and self-organized behavior. No internal/external centralized controls are required.
definition: Un sistema le cui componenti interagiscono dinamicamente e non linearmente, causando l’emergere di un comportamento collettivo, non banale e auto-organizzato. Non è richiesto nessun controllo centralizzato, né interno né esterno. @it
definition: Un système dont les composantes interagissent dynamiquement et non linéairement, causant l’émergence d’un comportement collectif, non trivial et auto-organisé. Aucun contrôle interne ou externe centralisé n’est requis. @fr
maturity: released

perspective
type: Class
subclass of: BFO_0000016
subclass of: Class
  intersection of: BFO_0000016
  intersection of: Restriction
    on property: BFO_0000164
    some values from: perspective information content entity
subclass of: Class
  intersection of: BFO_0000016
  intersection of: Restriction
    on property: disposition of
    some values from: Class
      union of: complex system environment component
      union of: complex system component
subclass of: Class
  intersection of: BFO_0000016
  intersection of: Restriction
    on property: is subject of
    some values from: perspective information content entity
comment: SCO currently accounts for perspectives of complex system components and complex system environment components because the focus of this ontology is on complex systems. Future versions of this ontology may explore extending reference more broadly to systems.
label: prospettiva @it
definition: A disposition whose realization leads the complex system component or the complex system environment component to (re)position itself within and regarding the complex system or complex system environment it belongs to (or a part of it) and possibly act accordingly.
definition: Una disposizione la cui realizzazione porta la componente del sistema complesso o la componente dell’ambiente del sistema complesso a (ri)posizionarsi nel e rispetto al sistema complesso o all’ ambiente del sistema complesso a cui appartiene (o parte di esso) ed eventualmente ad agire di conseguenza. @it
definition: Une disposition dont la réalisation conduit la composante de système complexe ou la composante de l’environnement du système complexe à se (re)positionner dans et par rapport au système complexe ou à l’environnement du système complexe auquel elle appartient (ou d’une partie de celui-ci) et, éventuellement, à agir en conséquence. @fr
maturity: released

indicator-role
type: Class
subclass of: BFO_0000023
subclass of: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: role of
    some values from: indicator
comment: To distinguish and account for indicators according to the perspectives of different complex systems (and environment) components, we suggest proceeding following the indications provided under the “according to the perspective” annotation property. In this case, regarding the subclasses to create, we recommend establishing axioms restricting to this class.
label: indicateur (rôle) @fr
label: ruolo di indicatore @it
see also: See the comments under the corresponding "indicator" class.
definition: A role whose realization leads the complex system component to be recognized as a carrier of an indicator value, by some complex system component or complex system environment component according to its/their perspective.
definition: Un rôle dont la réalisation conduit la composante de système complexe à être reconnu comme porteuse d’une valeur de l’indicateur, par quelque composante de système complexe ou de son l’environnement, selon sa/leur propre perspective. @fr
definition: un ruolo la cui realizzazione porta la componente del sistema complesso ad essere riconosciuto come portatore di un valore dell’indicatore, da parte di qualche componente del sistema complesso o del suo ambiente, secondo la propria prospettiva. @it
maturity: provisional

stakeholder-role
type: Class
subclass of: BFO_0000023
subclass of: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: role of
    some values from: stakeholder
label: ruolo di parte interessata (stakeholder) @it
label: rôle de partie prenante (stakeholder) @fr
definition: A role whose realization leads the complex system component to be recognized as a bearer, in the belonging complex system, of at least one role (different from the role of stakeholder) and/or disposition (primarily a disposition to benefit/be damaged as being part of that complex system).
definition: Un ruolo la cui realizzazione porta la componente del sistema complesso ad essere riconosciuta come detentrice, nel sistema complesso a cui appartiene, di almeno un ruolo (diverso dal ruolo di stakeholder) e/o disposizione (in primo luogo una predisposizione a beneficiare/essere danneggiata in quanto parte di tale sistema complesso). @it
definition: Un rôle dont la réalisation conduit la composante du système complexe à être reconnue, dans le système complexe auquel elle appartient, comme porteuse d’au moins un rôle (différent du rôle de partie prenante) et/ou d’une disposition (principalement une disposition à bénéficier ou à être endommagé parce qu’elle fait partie de ce système complexe). @fr
maturity: released

worth-role
type: Class
subclass of: BFO_0000023
subclass of: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: BFO_0000164
    some values from: worth information content entity
subclass of: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: is subject of
    some values from: worth information content entity
has_related_synonym: value
comment: Due to the SCO focus on complex systems, the worth-role class have been designed referring specifically to complex systems. Nevertheless, future implementations may broaden the space of application to also systems. Implementations may equally deepen this representation, detailing and elucidating the distinction and connection between worth and value(s).
comment: To distinguish and account for what is considered worthy of value for different complex systems (and environment) components according to proper perspectives,we suggest proceeding following the indications provided under the “according to the perspective” annotation property. In this case, regarding the subclasses to create, we recommend establishing axioms restricting to this class.
label: Valeur (sens donner de la valeur) @fr
label: valore (senso dare valore) @it
see also: (related) http://humanbehaviourchange.org/ontology/BCIO_006063
definition: A role whose realization leads the complex system or the complex system environment (or some part(s) of them) to be recognized to bearer relevance by some complex system component or complex system environment component according to its/their perspective.
definition: Un ruolo la cui realizzazione porta il sistema complesso o l'ambiente del sistema complesso (o una o più delle parti di essi) ad essere riconosciuto come rilevante da parte di qualche componente del sistema complesso o del suo ambiente, secondo la propria prospettiva. @it
definition: Un rôle dont la réalisation conduit le système complexe ou l’environnement de système complexe (ou une ou plus parties de ceux-ci) à être reconnu comme significatif par quelque composante de système complexe ou de son l’environnement, selon sa/leur propre perspective. @fr
maturity: released

interaction between complex system components and complex system environment components
type: Class
subclass of: interaction between system components and system environment components
subclass of: Class
  intersection of: interaction between system components and system environment components
  intersection of: Restriction
    on property: BFO_0000167
    some values from: complex system environment component
subclass of: Class
  intersection of: interaction between system components and system environment components
  intersection of: Restriction
    on property: BFO_0000167
    some values from: complex system component
subclass of: Class
  intersection of: interaction between system components and system environment components
  intersection of: Restriction
    on property: has agent at time t
    some values from: Class
      union of: complex system environment agent
      union of: complex system agent
subclass of: Class
  intersection of: interaction between system components and system environment components
  intersection of: Restriction
    on property: has agent at time t
    all values from: Class
      union of: complex system environment agent
      union of: complex system agent
disjoint with: interaction among complex system environment components
disjoint with: interaction among complex system components
has_related_synonym: relation between complex system components and complex system environment components, interconnection between complex system components and complex system environment components
label: Interaction entre les composantes de système complexe et les composantes de environnement de système complexe @fr
label: interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso @it
definition: An interaction that occurs between at least one complex system component and one complex system environment component where the latter belongs to the complex system environment of the complex system to which the complex system component belongs.
definition: Une interaction qui se produit entre au moins une composante d’un système complexe et au moins une composante de l’environnement du système complexe auquel la composante de système complexe appartient. @fr
definition: Un’interazione che avviene tra almeno una componente di un sistema complesso e almeno una componente dell’ambiente del sistema complesso a cui la componente del sistema complesso appartiene. @it
maturity: released

interaction among complex system environment components
type: Class
subclass of: interaction among system environment components
subclass of: Class
  intersection of: interaction among system environment components
  intersection of: Restriction
    on property: has agent at time t
    some values from: complex system environment agent
subclass of: Class
  intersection of: interaction among system environment components
  intersection of: Restriction
    on property: has agent at time t
    all values from: complex system environment agent
subclass of: Class
  intersection of: interaction among system environment components
  intersection of: Restriction
    on property: BFO_0000167
    min qualified cardinality: 2
    on class: complex system environment component
disjoint with: interaction among complex system components
has_related_synonym: relation among complex system environment components, interconnection among complex system environment components
label: interaction entre les composants de l’environnement de système complexe @fr
label: interazione tra le componenti dell’ambiente di sistema complesso @it
definition: An interaction that occurs among at least two complex system environment components.
definition: Une interaction qui se produit entre au moins deux composantes de l’environnement d’un système complexe. @fr
definition: Un’interazione che avviene tra almeno due componenti dell’ambiente di un sistema complesso. @it
maturity: released

interaction among complex system components
type: Class
subclass of: interaction among system components
subclass of: Class
  intersection of: interaction among system components
  intersection of: Restriction
    on property: has agent at time t
    some values from: complex system agent
subclass of: Class
  intersection of: interaction among system components
  intersection of: Restriction
    on property: has agent at time t
    all values from: complex system agent
subclass of: Class
  intersection of: interaction among system components
  intersection of: Restriction
    on property: BFO_0000167
    min qualified cardinality: 2
    on class: complex system component
has_related_synonym: relation among complex system components, interconnection among complex system components
label: Interaction entre les composantes de système complexe @fr
label: interazione tra le componenti del sistema complesso @it
definition: An interaction that occurs among at least two system components of a complex system.
definition: Une interaction qui se produit entre au moins deux composantes de système d’un système complexe. @fr
definition: Un’interazione che avviene tra almeno due componenti del sistema di un sistema complesso.
maturity: released

complex system history
type: Class
equivalent class: Class
  intersection of: system history
  intersection of: Restriction
    on property: BFO_0000184
    some values from: complex system
  intersection of: Restriction
    on property: BFO_0000184
    all values from: complex system
subclass of: system history
label: historie de système complexe @fr
label: storia del sistema complesso @it
definition: La storia del sistema di un sistema complesso. @it
definition: L’historique de système d’un système complexe. @fr
definition: The system history of a complex system.
maturity: released

system boundary
type: Class
equivalent class: Class
  intersection of: BFO_0000146
  intersection of: Restriction
    on property: BFO_0000137
    some values from: system
subclass of: BFO_0000146
comment: released
comment: Future SCO implementations may deal with representing system environment boudaries.
label: confine del sistema @it
label: frontière de système @fr
definition: A fiat surface of a system.
definition: Una superficie fiat di un sistema. @it
definition: Une surface fiat d’un système. @fr

system spatial region
type: Class
subclass of: BFO_0000028
comment: Future SCO implementations may consider including classes also covering spatial region for the system environment.
label: regione spaziale del sistema @it
label: région d’espace de système @fr
definition: A three-dimensional spatial region of a system.
definition: Una regione di spazio tridimensionale di un sistema. @it
definition: Une région d’espace tridimensionnelle d’un système. @fr
maturity: released

complex system environment component
type: Class
equivalent class: Class
  intersection of: system environment component
  intersection of: Restriction
    on property: BFO_0000176
    some values from: complex system environment
subclass of: system environment component
subclass of: Class
  intersection of: system environment component
  intersection of: Restriction
    on property: BFO_0000101
    some values from: perspective information content entity
subclass of: Class
  intersection of: system environment component
  intersection of: Restriction
    on property: has disposition
    some values from: perspective
disjoint with: complex system component
has_exact_synonym: complex system environment element
has_exact_synonym: complex system environment variable
label: componente dell' ambiente del systema complesso @it
label: composante de l'environnement de système complexe @fr
definition: A system evironment component that belongs to the system environment of a complex system.
definition: Una componente dell'ambiente di sistema che appartiene all’ambiente di un sistema complesso. @it
definition: Une composante de l'environnement de système qui appartient à l’environnement d’un système complexe. @fr
maturity: released

system environnement agent
type: Class
equivalent class: Class
  intersection of: system environment component
  intersection of: Restriction
    on property: agent in at time t
    some values from: Class
      union of: interaction among system environment components
      union of: interaction between system components and system environment components
  intersection of: Restriction
    on property: agent in at time t
    all values from: Class
      union of: interaction among system environment components
      union of: interaction between system components and system environment components
subclass of: system environment component
disjoint with: system agent
comment: We envision revisions of the current SCO theory of agency. This is due to the limited power of explainability of present representation. A sounder and deeper interpretation of the causal role of an agent in an interaction, compared to other participants, is required. Tentative proposal: a possible direction of implementation is towards a telic vision of agency intended as end-point driven. On this more fundamental neutral vision, a second layer of representation may be constructed to model intentionality, goals, and plans in relation to agency. Here, SCO may harmonize and align with UFO-C representation. For insight for discussion see: Guarino, N., & Guizzardi, G. (2024). Processes as variable embodiments. Synthese, 203(4), 104. https://doi.org/10.1007/s11229-024-04505-2 Guizzardi, G., de Almeida Falbo, R., & Guizzardi, R. (2008). Grounding software domain ontologies in the unified foundational ontology (UFO): The case of the ODE. Memorias de la XI Conferencia Iberoamericana de Software Engineering (CIbSE 2008), Recife, Pernambuco, Brasil, February 13-17, 2008, 127–140.
label: agent de l’environnement de système @fr
label: agente dell’ambiente del sistema @it
see also: comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029
see also: See information under the "has agent at t" property.
definition: A system environment component that is an agent in an interaction among system environment components or in an interaction between system components and system environment components.
definition: Una componente dell’ambiente del sistema che è un agente in un'interazione tra le componenti dell'ambiente del sistema o in un'interazione tra componenti del sistema e le componenti dell'ambiente del sistema. @it
definition: Une composante de l’environnement de système qui est un agent dans une interaction entre les composantes de l’environnement du système ou dans une interaction entre les composantes de système et les composants de l’environnement de système. @fr
maturity: provisional

complex system component
type: Class
equivalent class: Class
  intersection of: system component
  intersection of: Restriction
    on property: BFO_0000176
    some values from: complex system
subclass of: system component
subclass of: Class
  intersection of: system component
  intersection of: Restriction
    on property: BFO_0000101
    some values from: perspective information content entity
subclass of: Class
  intersection of: system component
  intersection of: Restriction
    on property: has disposition
    some values from: perspective
has_exact_synonym: complex system element
has_related_synonym: complex system variable
label: componente del sistema complesso @it
label: composante de système complexe @fr
definition: A system component that belongs to a complex system.
definition: Una componente del sistema che appartiene a un sistema complesso. @it
definition: Une composante de système qui appartient à un système complexe. @fr
maturity: released

system agent
type: Class
equivalent class: Class
  intersection of: system component
  intersection of: Restriction
    on property: agent in at time t
    some values from: Class
      union of: interaction among system components
      union of: interaction between system components and system environment components
  intersection of: Restriction
    on property: agent in at time t
    all values from: Class
      union of: interaction among system components
      union of: interaction between system components and system environment components
subclass of: system component
comment: We envision revisions of the current SCO theory of agency. This is due to the limited power of explainability of present representation. A sounder and deeper interpretation of the causal role of an agent in an interaction, compared to other participants, is required. Tentative proposal: a possible direction of implementation is towards a telic vision of agency intended as end-point driven. On this more fundamental neutral vision, a second layer of representation may be constructed to model intentionality, goals, and plans in relation to agency. Here, SCO may harmonize and align with UFO-C representation. For insight for discussion see: Guarino, N., & Guizzardi, G. (2024). Processes as variable embodiments. Synthese, 203(4), 104. https://doi.org/10.1007/s11229-024-04505-2 Guizzardi, G., de Almeida Falbo, R., & Guizzardi, R. (2008). Grounding software domain ontologies in the unified foundational ontology (UFO): The case of the ODE. Memorias de la XI Conferencia Iberoamericana de Software Engineering (CIbSE 2008), Recife, Pernambuco, Brasil, February 13-17, 2008, 127–140.
label: agent de système @fr
label: agente del sistema @it
see also: comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029
see also: See information under the "has agent at t" property.
definition: A system component that is an agent in an interaction among system components or in an interaction between system components and system environment components.
definition: Una componente di sistema che è un agente in un'interazione tra le componenti del sistema o in un'interazione tra le componenti di sistema e le componenti dell'ambiente di sistema. @it
definition: Une composante de système qui est un agent dans une interaction entre les composantes de l’environnement du système ou dans une interaction entre les composantes de système et les composants de l’environnement de système. @fr
maturity: provisional

stakeholder perspective
type: Class
equivalent class: Class
  intersection of: perspective
  intersection of: Restriction
    on property: disposition of
    some values from: stakeholder
subclass of: perspective
subclass of: Class
  intersection of: perspective
  intersection of: Restriction
    on property: BFO_0000164
    some values from: stakeholder perspective information content entity
subclass of: Class
  intersection of: perspective
  intersection of: Restriction
    on property: is subject of
    some values from: stakeholder perspective information content entity
has_exact_synonym: complex system stakeholder perspective, system stakeholder perspective
label: Prospettiva di parte interessata (stakeholder) @it
label: perspective de partie prenante (stakeholder) @fr
definition: A perspective that is bearered by a stakeholder.
definition: Una prospettiva che è detenuta da una parte interessata (stakeholder). @it
definition: Une perspective qui est détenue par une partie prenante (stakeholder). @fr
maturity: released

complex system boundary
type: Class
equivalent class: Class
  intersection of: system boundary
  intersection of: Restriction
    on property: BFO_0000137
    some values from: complex system
subclass of: system boundary
label: confine del sistema complesso @it
label: frontière de système complexe @fr
definition: A system boundary of a complex system.
definition: Un confine del sistema di un sistema complesso. @it
definition: Une frontière de système d’un système complexe. @fr
maturity: released

complex system spatial region
type: Class
subclass of: system spatial region
label: regione spaziale del sistema complesso @it
label: région d’espace de système complexe @fr
definition: A system spatial region of a complex system.
definition: Una regione di spazio del sistema di un sistema complesso. @it
definition: Une région d’espace de système d’un système complexe. @fr
maturity: released

complex system environment agent
type: Class
equivalent class: Class
  intersection of: complex system environment component
  intersection of: Restriction
    on property: agent in at time t
    some values from: Class
      union of: interaction between complex system components and complex system environment components
      union of: interaction among complex system environment components
  intersection of: Restriction
    on property: agent in at time t
    all values from: Class
      union of: interaction between complex system components and complex system environment components
      union of: interaction among complex system environment components
subclass of: system environnement agent
disjoint with: complex system agent
label: agent de l’environnement de système complexe @fr
label: agente dell’ambiente del sistema complesso @it
see also: See information under the "has agent at t" property.
definition: A complex system environment component that is an agent in an interaction among complex system environment components or in an interaction between complex system components and complex system environment components.
definition: Una componente dell’ambiente del sistema complesso che è un agente in un'interazione tra componenti dell’ambiente del sistema complesso o in un'interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso. @it
definition: Une composante de l’environnement de système complexe qui est un agent dans une interaction entre les composantes de l’environnement de système complexe ou dans une interaction entre les composantes de système complexe et les composantes de l’environnement de système complexe. @fr
maturity: released

complex system agent
type: Class
equivalent class: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: agent in at time t
    some values from: Class
      union of: interaction between complex system components and complex system environment components
      union of: interaction among complex system components
  intersection of: Restriction
    on property: agent in at time t
    all values from: Class
      union of: interaction between complex system components and complex system environment components
      union of: interaction among complex system components
subclass of: system agent
label: agent de système complexe @fr
label: agente del sistema complesso @it
see also: See information under the "has agent at t" property.
definition: A complex system component that is an agent in an interaction among complex system components or in an interaction between complex system components and complex system environment components.
definition: Una componente del sistema complesso che è un agente in un'interazione tra le componenti del sistema complesso o in un'interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso. @it
definition: Une composante de système complexe qui est un agent dans une interaction entre les composantes de système complexe ou dans une interaction entre les composantes de système complexe et les composantes de l’environnement de système complexe. @fr
maturity: released

indicator
type: Class
equivalent class: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: has role
    some values from: indicator-role
subclass of: complex system component
subclass of: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: BFO_0000220
    some values from: indicator value
subclass of: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: represented by
    some values from: indicator value
has_exact_synonym: complex system indicator
has_related_synonym: system indicator
comment: SCO indicator classes have been designed referring to the characterization of sustainable development indicators (SDGs indicators) proposed by SDGIO. we aimed to deepen this characterization and establish upper-level classes for SDGIO ones.
comment: Due to the SCO focus on complex systems, indicator classes have been designed referring specifically to complex systems. Nevertheless, future implementations may broaden the space of application to also systems.
label: indicateur @fr
label: indicatore @it
definition: A complex system component with an indicator role.
definition: Una componente del sistema complesso con un ruolo d’indicatore. @it
definition: Une composante de système complexe ayant un rôle d’indicateur. @fr
maturity: provisional

stakeholder
type: Class
equivalent class: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: has role
    some values from: stakeholder-role
subclass of: complex system component
subclass of: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: BFO_0000101
    some values from: stakeholder perspective information content entity
subclass of: Class
  intersection of: complex system component
  intersection of: Restriction
    on property: has disposition
    some values from: stakeholder perspective
has_exact_synonym: complex system stakeholder, system stakeholder
label: parte interessata (stakeholder) @it
label: partie prenante (stakeholder) @fr
definition: A complex system component with a stakeholder role.
definition: Una componente del sistema complesso con un ruolo di stakeholder. @it
definition: Une composante du système complexe avec un rôle de partie prenante. @fr
maturity: released

stakeholder perspective information content entity
type: Class
equivalent class: Class
  intersection of: perspective information content entity
  intersection of: Restriction
    on property: is about
    some values from: stakeholder perspective
subclass of: perspective information content entity
subclass of: Class
  intersection of: perspective information content entity
  intersection of: Restriction
    on property: BFO_0000084
    some values from: stakeholder
subclass of: Class
  intersection of: perspective information content entity
  intersection of: Restriction
    on property: BFO_0000165
    some values from: stakeholder perspective
label: contenu informatif de la perspective de partie prenante (stakeholder) @fr
label: contenuto informativo della prospettiva di parte interessata (stakeholder) @it
definition: A perspective information content entity of a stakeholder perspective.
definition: Un contenu informatif de la perspective d’une perspective de partie prenante (stakeholder). @fr
definition: Un contenuto informativo della prospettiva di una prospettiva di parte interessata (stakeholder). @it
maturity: released

complex system property
type: Class
subclass of: BFO_0000020
comment: Do not use this class directly. This class is constructed as a grouping for complex system properties, such as emergence and self-organization, in order to facilitate class retrieval and visualization.
label: proprietà del systema complesso @it
definition: propriété de système complexe @fr
maturity: released

emergence
type: Class
subclass of: complex system property
subclass of: Class
  intersection of: BFO_0000019
  intersection of: Restriction
    on property: quality of
    some values from: complex system
disjoint with: self-organization
comment: A more extensive representation of emergence is required. A possible starting point may be the work of Calhau et al. (2024). Calhau, R. F., Prince Sales, T., Oliveira, Í., Kokkula, S., Ferreira Pires, L., Cameron, D., Guizzardi, G., & Almeida, J. P. A. (2024). A System Core Ontology for Capability Emergence Modeling. In H. A. Proper, L. Pufahl, D. Karastoyanova, M. Van Sinderen, & J. Moreira (A c. Di), Enterprise Design, Operations, and Computing (Vol. 14367, pp. 3–20). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-46587-1_1
comment: This class should be amended according to SCO implementations regarding system scales, levels, and change.
label: emergenza (proprietà emergenti) @it
label: émergence (propriété émergentes @fr
definition: A quality that inherits in a complex system by virtue of how the complex system behavior and properties at a macroscopic level are nontrivially envisaged from those at a more microscopic one.
definition: Una qualità che il sistema complesso esibisce in virtù del fatto che il comportamento del sistema complesso e le sue proprietà a un livello macroscopico sono non-trivialmente predicibili da quelli a livello più microscopico. @it
definition: Une qualité qu’un système complexe exhibe en vertu du fait que le comportement du système complexe et ses propriétés à un niveau macroscopique sont non-trivialement prédictibles à partir de ceux aux niveaux plus microscopiques. @fr
maturity: provisional

self-organization
type: Class
subclass of: complex system property
subclass of: Class
  intersection of: BFO_0000019
  intersection of: Restriction
    on property: quality of
    some values from: complex system
comment: This class should be amended according to SCO implementations regarding system scales, levels, and change.
label: auto-organisation @fr
label: auto-organizzazione @it
definition: A quality that inherits in a complex system by virtue of how the complex system components spontaneously arrange, globally generating macroscopic and microscopic structures and behaviors, without any internal and/or external controls.
definition: Una qualità che il sistema complesso esibisce in virtù del fatto che le componenti del sistema complesso si organizzino spontaneamente, generando globalmente strutture e comportamenti macroscopici e microscopici, senza alcun controllo interno e/o esterno. @it
definition: Une qualité qu’un système complexe exhibe en vertu du fait que les composantes du système complexe s’organisent spontanément, générant globalement des structures et comportements macroscopiques et microscopiques, sans aucun contrôle interne et/ou externe. @fr
maturity: provisional

provisional
type: NamedIndividual
type: maturity level
definition: construct or ontology development state in which content is subject to change and may change considerably
explanatory note: IOF users should be aware that the resource is not dependable, but can be used for reference and for further work.

released
type: NamedIndividual
type: maturity level
definition: construct or ontology development state in which the resource is stable, usable, and has been made available to external users
explanatory note: Release notes will be provided for any changes concerning released content, and any revisions will be backward compatible with the prior version to the degree possible.

BFO_0000002
textual definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

BFO_0000003
textual definition: An entity that has temporal parts and that happens, unfolds or develops through time.

BFO_0000017
textual definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.

BFO_0000050
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
textual definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative label: part_of

BFO_0000051
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
textual definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative label: has_part

BFO_0000054
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])

BFO_0000055
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])

BFO_0000062
editor preferred term: preceded by
textual definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative label: is preceded by
alternative label: preceded_by

BFO_0000063
editor preferred term: precedes
textual definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

BFO_0000066
editor preferred term: occurs in
textual definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative label: occurs_in
alternative label: unfolds in
alternative label: unfolds_in

BFO_0000067
editor preferred term: site of
textual definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t

CL_0000000
textual 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.
textual definition: A material entity that has a plasma membrane and results from cellular division.

Axiom
annotated source: CL_0000000
annotated property: textual definition
annotated target: 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.
has db xref: CARO:mah

CL_0000101
textual definition: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.

Axiom
annotated source: CL_0000101
annotated property: textual definition
annotated target: Any neuron having a sensory function; an afferent neuron conveying sensory impulses.
has db xref: ISBN:0721662544

CL_0000540
textual definition: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
has_exact_synonym: nerve cell

Axiom
annotated source: CL_0000540
annotated property: textual definition
annotated target: The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
has db xref: MESH:D009474
has db xref: http://en.wikipedia.org/wiki/Neuron

COB_0001000
textual definition: A process during which an organism comes into contact with another entity.

ENVO_01000254
textual definition: A system which has the disposition to environ one or more material entities.
has_exact_synonym: environment

Axiom
annotated source: ENVO_01000254
annotated property: textual definition
annotated target: A system which has the disposition to environ one or more material entities.
has db xref: DOI:10.1186/2041-1480-4-43

ENVO_01000739
textual definition: An environmental system which can sustain and allow the growth of an ecological population.

Axiom
annotated source: ENVO_01000739
annotated property: textual definition
annotated target: An environmental system which can sustain and allow the growth of an ecological population.
has db xref: EnvO:EnvO

ENVO_01003004
textual definition: A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.

GO_0003674
textual definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has_exact_synonym: molecular function

Axiom
annotated source: GO_0003674
annotated property: textual definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has db xref: GOC:pdt

GO_0004842
textual definition: Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
has_broad_synonym: E2
has_broad_synonym: E3
has_narrow_synonym: ubiquitin conjugating enzyme activity
has_narrow_synonym: ubiquitin ligase activity
has_narrow_synonym: ubiquitin protein ligase activity
has_narrow_synonym: ubiquitin protein-ligase activity
has_narrow_synonym: ubiquitin-conjugating enzyme activity

Axiom
annotated source: GO_0004842
annotated property: textual definition
annotated target: Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
has db xref: GOC:BioGRID
has db xref: GOC:jh2
has db xref: PMID:9635407

GO_0005634
textual 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.
has_exact_synonym: cell nucleus
has_narrow_synonym: horsetail nucleus

Axiom
annotated source: GO_0005634
annotated property: textual definition
annotated target: 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.
has db xref: GOC:go_curators

Axiom
annotated source: GO_0005634
annotated property: has_narrow_synonym
annotated target: horsetail nucleus
has db xref: GOC:al
has db xref: GOC:mah
has db xref: GOC:vw
has db xref: PMID:15030757

GO_0008150
textual definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
textual definition: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_related_synonym: single organism process
has_related_synonym: single-organism process

Axiom
annotated source: GO_0008150
annotated property: textual definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
has db xref: GOC:pdt

GO_0016301
textual definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has_exact_synonym: phosphokinase activity

Axiom
annotated source: GO_0016301
annotated property: textual definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has db xref: ISBN:0198506732

GO_0019107
textual definition: Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.

Axiom
annotated source: GO_0019107
annotated property: textual definition
annotated target: Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
has db xref: GOC:ai

IAO_0000002
editor preferred term: example to be eventually removed

IAO_0000027
editor preferred term: data item

IAO_0000030
editor preferred term: information content entity

IAO_0000078
editor preferred term: curation status specification
has curation status: IAO_0000125
textual definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

IAO_0000102
editor preferred term: data about an ontology part
textual definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg

IAO_0000103
editor preferred term: failed exploratory term
textual definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

IAO_0000113
editor preferred term: in branch
textual definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

IAO_0000120
editor preferred term: metadata complete
textual definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

IAO_0000121
editor preferred term: organizational term
textual definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

IAO_0000122
editor preferred term: ready for release
has curation status: IAO_0000125
textual definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

IAO_0000123
editor preferred term: metadata incomplete
textual definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

IAO_0000124
editor preferred term: uncurated
textual definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

IAO_0000125
editor preferred term: pending final vetting
textual definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

IAO_0000224
textual definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

IAO_0000225
editor preferred term: obsolescence reason specification
has curation status: IAO_0000125
textual definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

IAO_0000226
editor preferred term: placeholder removed

IAO_0000227
editor preferred term: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

IAO_0000228
editor preferred term: term imported
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

IAO_0000229
editor preferred term: term split
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

IAO_0000231
editor preferred term: has obsolescence reason
textual definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

IAO_0000234
editor preferred term: ontology term requester
has curation status: IAO_0000125
textual definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg

IAO_0000409
editor preferred term: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
textual definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

IAO_0000410
editor preferred term: universal
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

IAO_0000411
editor preferred term: is denotator type
textual definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

IAO_0000412
editor preferred term: imported from
has curation status: IAO_0000125
textual definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

IAO_0000420
editor preferred term: defined class
textual definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
term editor: Alan Ruttenberg

IAO_0000421
editor preferred term: named class expression
textual definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
term editor: Alan Ruttenberg

IAO_0000423
editor preferred term: to be replaced with external ontology term
textual definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

IAO_0000425
editor preferred term: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
textual definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

IAO_0000426
editor preferred term: first order logic expression
textual definition: An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.
term editor: PERSON:Alan Ruttenberg

IAO_0000427
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
textual definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg

IAO_0000428
editor preferred term: requires discussion
has curation status: IAO_0000125
textual definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI

IAO_0000589
editor preferred term: OBO foundry unique label
has curation status: IAO_0000125
textual definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

IAO_0000596
editor preferred term: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
textual definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

IAO_0000597
editor preferred term: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
textual definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

IAO_0000598
editor preferred term: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
textual definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

IAO_0000599
editor preferred term: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
textual definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

IAO_0000601
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

IAO_0000602
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

IAO_0000603
editor preferred term: is allocated id range
textual definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg

IAO_0000700
editor preferred term: has ontology root term
textual definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

IAO_0006011
editor preferred term: may be identical to
textual definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland

IAO_0006012
editor preferred term: scheduled for obsoletion on or after
textual definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng

IAO_0010000
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

IAO_0100001
editor preferred term: term replaced by
has curation status: IAO_0000125
textual definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

IAO_8000000
editor preferred term: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative label: ontology file

IAO_8000001
editor preferred term: base ontology module
textual definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

IAO_8000002
editor preferred term: editors ontology module
textual definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative label: source ontology module

IAO_8000003
editor preferred term: main release ontology module
textual definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

IAO_8000004
editor preferred term: bridge ontology module
textual definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

IAO_8000005
editor preferred term: import ontology module
textual definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

IAO_8000006
editor preferred term: subset ontology module
textual definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

IAO_8000007
editor preferred term: curation subset ontology module
textual definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

IAO_8000008
editor preferred term: analysis ontology module
textual definition: An ontology module that is intended for usage in analysis or discovery applications.

IAO_8000009
editor preferred term: single layer ontology module
textual definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative label: ribbon subset

IAO_8000010
editor preferred term: exclusion subset ontology module
textual definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

IAO_8000011
editor preferred term: external import ontology module
textual definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

IAO_8000012
editor preferred term: species subset ontology module
textual definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

IAO_8000013
editor preferred term: reasoned ontology module
textual definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

IAO_8000014
editor preferred term: generated ontology module
textual definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

IAO_8000015
editor preferred term: template generated ontology module
textual definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

IAO_8000016
editor preferred term: taxonomic bridge ontology module

IAO_8000017
editor preferred term: ontology module subsetted by expressivity

IAO_8000018
editor preferred term: obo basic subset ontology module
textual definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

IAO_8000019
editor preferred term: ontology module subsetted by OWL profile

IAO_8000020
editor preferred term: EL++ ontology module

OBI_0000011
editor preferred term: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
textual definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived

OBI_0000047
editor preferred term: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: IAO_0000122
textual definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

OBI_0000070
editor preferred term: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
textual definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
term editor: PlanAndPlannedProcess Branch
alternative label: measuring
alternative label: scientific observation
definition source: OBI branch derived

OBI_0000967
editor preferred term: container
has curation status: IAO_0000123
textual definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
term editor: PERSON: Bjoern Peters

OBI_0000968
editor preferred term: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: IAO_0000122
textual definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI development call 2012-12-17.

OBI_0100026
editor preferred term: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: IAO_0000122
textual definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

OGMS_0000031
textual definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

OMO_0001000
textual definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
term editor: http://orcid.org/0000-0001-5208-3432

OMO_0001001
textual definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call

OMO_0002000
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
textual definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963

OMO_0003000
example of usage: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
textual definition: A synonym type for describing abbreviations or initalisms

OMO_0003001
textual definition: A synonym type for describing ambiguous synonyms

OMO_0003002
textual definition: A synonym type for describing dubious synonyms

OMO_0003003
example of usage: EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)
textual definition: A synonym type for describing layperson or colloquial synonyms

OMO_0003004
example of usage: CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)
textual definition: A synonym type for describing pluralization synonyms

OMO_0003005
example of usage: CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)
textual definition: A synonym type for describing UK spelling variants

OMO_0003006
textual definition: A synonym type for common misspellings

OMO_0003007
textual definition: A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway

OMO_0003008
example of usage: MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.
textual definition: A synonym type for names that have been used as primary labels in the past.

OMO_0003009
example of usage: The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College
textual definition: A synonym type for the legal entity name

PATO_0000001
textual definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities

Axiom
annotated source: PATO_0000001
annotated property: textual definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

PATO_0000402
textual definition: A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
has_exact_synonym: ramified
has_exact_synonym: ramiform

Axiom
annotated source: PATO_0000402
annotated property: textual definition
annotated target: A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
has db xref: WordNet:WordNet

PATO_0001199
textual definition: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.

Axiom
annotated source: PATO_0001199
annotated property: textual definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
has db xref: ISBN:0881923214

PATO_0001470
textual definition: A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.
has_exact_synonym: proportion
has_exact_synonym: proportionality
has_exact_synonym: quotient
has_exact_synonym: ratio
has_related_synonym: rate

Axiom
annotated source: PATO_0001470
annotated property: textual definition
annotated target: A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity.
has db xref: PATOC:nw

PATO_0002124
textual definition: A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.

Axiom
annotated source: PATO_0002124
annotated property: textual definition
annotated target: A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
has db xref: PATOC:GVG

RO_0000056
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
textual definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in

RO_0000057
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
textual definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative label: has_participant

RO_0000058
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
textual definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

RO_0000059
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
textual definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

RO_0000300
has curation status: IAO_0000125
textual definition: OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0000301
has curation status: IAO_0000125
textual definition: OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0000302
has curation status: IAO_0000125
textual definition: OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0001000
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: IAO_0000125
textual definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative label: derives_from

RO_0001001
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: IAO_0000125
textual definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative label: derives_into

RO_0001015
editor preferred term: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
textual definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
alternative label: location_of

RO_0001018
editor preferred term: contained in
editor note: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
editor note: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
alternative label: contained_in

RO_0001019
editor preferred term: contains

RO_0001020
example of usage: penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
textual definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

RO_0001021
textual definition: A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

RO_0001022
example of usage: penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
textual definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

RO_0001023
textual definition: A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.

RO_0001901
textual definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

RO_0001902
textual definition: ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y)

RO_0002000
example of usage: the surface of my skin is a 2D boundary of my body
textual definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative label: 2D_boundary_of
alternative label: boundary of
alternative label: is 2D boundary of
alternative label: is boundary of
alternative label: surface of

RO_0002001
has curation status: IAO_0000125
editor note: May be obsoleted, see https://github.com/oborel/obo-relations/issues/260
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002002
example of usage: my body has 2D boundary the surface of my skin
textual definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: has boundary
alternative label: has_2D_boundary

RO_0002003
textual definition: A relation that holds between two neurons that are electrically coupled via gap junctions.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002004
textual definition: The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002007
textual definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002008
textual definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
editor note: Note from NCEAS meeting: consider changing primary label
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002009
textual definition: A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002010
textual definition: x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
term editor: https://orcid.org/0000-0002-7073-9172
has_exact_synonym: regulates in other organism

RO_0002011
textual definition: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002012
textual definition: A part of relation that applies only between occurrents.

RO_0002013
textual definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.

RO_0002014
textual definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.

RO_0002015
textual definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.

RO_0002018
textual definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.

RO_0002019
textual definition: A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.

RO_0002020
textual definition: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.

RO_0002021
textual definition: A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.

RO_0002023
textual definition: Process(P2) is directly negatively regulated by process(P1) 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 P2 directly negatively regulated by P1.

Axiom
annotated source: RO_0002023
annotated property: textual definition
annotated target: Process(P2) is directly negatively regulated by process(P1) 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 P2 directly negatively regulated by P1.
has db xref: https://orcid.org/0000-0002-7073-9172

RO_0002024
textual definition: Process(P2) is directly postively regulated by process(P1) 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 P2 is directly postively regulated by P1.

Axiom
annotated source: RO_0002024
annotated property: textual definition
annotated target: Process(P2) is directly postively regulated by process(P1) 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 P2 is directly postively regulated by P1.
has db xref: https://orcid.org/0000-0002-7073-9172

RO_0002025
textual definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.

Axiom
annotated source: RO_0002025
annotated property: textual definition
annotated target: 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.
has db xref: https://orcid.org/0000-0002-7073-9172

RO_0002026
textual definition: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.

Axiom
annotated source: RO_0002026
annotated property: textual definition
annotated target: A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.
has db xref: https://orcid.org/0000-0002-7073-9172

RO_0002029
textual definition: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.

Axiom
annotated source: RO_0002029
annotated property: textual definition
annotated target: Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.
has db xref: PMID:24138933
has db xref: Wikipedia:Infant_mortality

RO_0002081
term editor: David Osumi-Sutherland
alternative label: <=

RO_0002082
textual definition: x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.
term editor: https://orcid.org/0000-0002-7073-9172
term editor: David Osumi-Sutherland

RO_0002083
term editor: David Osumi-Sutherland

RO_0002084
term editor: David Osumi-Sutherland

RO_0002085
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: di

RO_0002086
term editor: David Osumi-Sutherland

RO_0002087
term editor: David Osumi-Sutherland
alternative label: starts_at_end_of

RO_0002088
term editor: David Osumi-Sutherland

RO_0002089
term editor: David Osumi-Sutherland

RO_0002090
term editor: https://orcid.org/0000-0002-7073-9172
term editor: David Osumi-Sutherland
alternative label: ends_at_start_of
alternative label: meets

RO_0002091
term editor: David Osumi-Sutherland
alternative label: io

RO_0002092
term editor: David Osumi-Sutherland
alternative label: d
alternative label: during

RO_0002093
term editor: David Osumi-Sutherland
alternative label: o
alternative label: overlaps

RO_0002100
has curation status: IAO_0000125
textual definition: Relation between a neuron and a material anatomical entity that its soma is part of.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002101
has curation status: IAO_0000125
textual definition: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: fasciculates with

RO_0002102
has curation status: IAO_0000125
textual definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002103
has curation status: IAO_0000125
textual definition: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002104
example of usage: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
has curation status: IAO_0000125
textual definition: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
term editor: https://orcid.org/0000-0001-9990-8331
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-1617-8244
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19243617

RO_0002105
has curation status: IAO_0000125
textual definition: A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002106
has curation status: IAO_0000125
textual definition: A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002107
has curation status: IAO_0000125
textual definition: A relation between a motor neuron and a muscle that it synapses to via a type II bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002108
has curation status: IAO_0000125
textual definition: Relation between a muscle and a motor neuron that synapses to it via a type II bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002109
has curation status: IAO_0000125
textual definition: Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002110
has curation status: IAO_0000125
textual definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: synapsed in

RO_0002111
has curation status: IAO_0000125
alternative label: has neurotransmitter

RO_0002112
has curation status: IAO_0000125
textual definition: Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.
term editor: https://orcid.org/0000-0001-5948-3092
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002113
has curation status: IAO_0000125
textual definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
alternative label: synapses in

RO_0002114
textual definition: A relation between a motor neuron and a muscle that it synapses to via a type III bouton.

RO_0002115
textual definition: Relation between a muscle and a motor neuron that synapses to it via a type III bouton.

RO_0002120
has curation status: IAO_0000125
textual definition: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002121
has curation status: IAO_0000125
textual definition: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002130
has curation status: IAO_0000125
textual definition: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: has synapse in

RO_0002131
has curation status: IAO_0000125
textual definition: x overlaps y if and only if there exists some z such that x has part z and z part of y

RO_0002132
has curation status: IAO_0000125
textual definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: has fasciculating component

RO_0002134
has curation status: IAO_0000125
textual definition: Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
term editor: https://orcid.org/0000-0002-7073-9172

RO_0002150
has curation status: IAO_0000125
textual definition: X continuous_with Y if and only if X and Y share a fiat boundary.
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: connected to

RO_0002151
has curation status: IAO_0000125
textual definition: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
editor note: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
alternative label: proper overlaps

RO_0002156
has curation status: IAO_0000125
textual definition: d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
alternative label: ancestral_stucture_of
alternative label: evolutionarily_descended_from

RO_0002157
has curation status: IAO_0000125
textual definition: inverse of derived by descent from

RO_0002158
has curation status: IAO_0000125
textual definition: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.

RO_0002160
example of usage: lactation SubClassOf 'only in taxon' some 'Mammalia'
has curation status: IAO_0000125
textual definition: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
editor note: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947

RO_0002161
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
textual definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947

RO_0002162
has curation status: IAO_0000125
textual definition: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
term editor: 0000-0001-9227-417X
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947

RO_0002170
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
textual definition: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

RO_0002171
textual definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
alternative label: non-overlapping with
alternative label: shares no parts with
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

RO_0002172
textual definition: An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.

RO_0002173
textual definition: S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]

RO_0002174
textual definition: S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

RO_0002175
textual definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

RO_0002176
example of usage: The M8 connects Glasgow and Edinburgh
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
textual definition: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

RO_0002177
textual definition: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.

RO_0002178
textual definition: Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

RO_0002179
textual definition: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

RO_0002180
has curation status: IAO_0000125
textual definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.

RO_0002200
has curation status: IAO_0000125
textual definition: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002201
has curation status: IAO_0000125
textual definition: inverse of has phenotype
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002202
has curation status: IAO_0000125
textual definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
term editor: https://orcid.org/0000-0001-9114-8737
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
term editor: https://orcid.org/0000-0003-1980-3228

RO_0002203
has curation status: IAO_0000125
textual definition: inverse of develops from
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
term editor: https://orcid.org/0000-0003-1980-3228

RO_0002204
has curation status: IAO_0000125
textual definition: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
editor note: We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002205
example of usage: every HOTAIR lncRNA is the gene product of some HOXC gene
example of usage: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
has curation status: IAO_0000125
textual definition: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002206
example of usage: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
has curation status: IAO_0000125
textual definition: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002207
has curation status: IAO_0000125
textual definition: Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
definition source: FBbt
has_exact_synonym: has developmental precursor

RO_0002208
textual definition: A parasite that kills or sterilizes its host

RO_0002209
textual definition: inverse of parasitoid of

RO_0002210
has curation status: IAO_0000125
textual definition: inverse of directly develops from
alternative label: developmental precursor of

RO_0002211
textual definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
term editor: https://orcid.org/0000-0001-7476-6306
term editor: https://orcid.org/0000-0002-3837-8864
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
definition source: GO
elucidation: false

RO_0002212
textual definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002213
textual definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002214
example of usage: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
has curation status: IAO_0000125
textual definition: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
editor note: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
editor note: TODO: add homeomorphy axiom
editor note: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002215
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
textual definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450

RO_0002216
textual definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function in

RO_0002217
textual definition: OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: agent in

RO_0002218
textual definition: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has agent

RO_0002219
has curation status: IAO_0000125
textual definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002220
example of usage: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
has curation status: IAO_0000125
textual definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
term editor: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: RO_0002220
annotated property: example of usage
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

RO_0002221
has curation status: IAO_0000125
textual definition: inverse of surrounded by
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002223
has curation status: IAO_0000125
textual definition: inverse of starts with
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
definition source: Allen

RO_0002224
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: IAO_0000125
textual definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
alternative label: started by

RO_0002225
has curation status: IAO_0000125
textual definition: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002226
has curation status: IAO_0000125
textual definition: x develops_in y if x is located in y whilst x is developing
term editor: https://orcid.org/0000-0002-6601-2165
definition source: EHDAA2
definition source: Jonathan Bard, EHDAA2

RO_0002227
textual definition: A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.

RO_0002228
textual definition: A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.

RO_0002229
has curation status: IAO_0000125
textual definition: inverse of ends with
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall

RO_0002230
has curation status: IAO_0000125
textual definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall
alternative label: finished by

RO_0002231
has curation status: IAO_0000125
textual definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: starts with process that occurs in

RO_0002232
has curation status: IAO_0000125
textual definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: ends with process that occurs in

RO_0002233
has curation status: IAO_0000125
textual definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: consumes

RO_0002234
has curation status: IAO_0000125
textual definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: produces

RO_0002235
textual definition: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)

RO_0002236
textual definition: A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)

RO_0002237
textual definition: A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.

RO_0002238
textual definition: X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.

RO_0002240
textual definition: A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
definition source: ExO:0000001

RO_0002241
textual definition: A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
definition source: ExO:0000000

RO_0002242
textual definition: A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
definition source: ExO:0000055

RO_0002243
textual definition: A broad relationship between an exposure event or process and the course takes from the source to the target.
definition source: http://purl.obolibrary.org/obo/ExO_0000004

RO_0002244
textual definition: Any relationship between an exposure event or process and any other entity.

RO_0002245
textual definition: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.

RO_0002246
textual definition: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

RO_0002248
example of usage: Any portion of roundup 'has active ingredient' some glyphosate
textual definition: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
has_exact_synonym: has active substance
has_related_synonym: has active pharmaceutical ingredient

RO_0002249
textual definition: inverse of has active ingredient

RO_0002252
example of usage: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
textual definition: b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.

RO_0002253
textual definition: inverse of connecting branch of

RO_0002254
example of usage: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
has curation status: IAO_0000125
textual definition: x has developmental contribution from y iff x has some part z such that z develops from y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002255
has curation status: IAO_0000125
textual definition: inverse of has developmental contribution from
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002256
has curation status: IAO_0000125
textual definition: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
term editor: https://orcid.org/0000-0001-9114-8737
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: induced by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
definition source: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
definition source: GO:0001759

RO_0002257
has curation status: IAO_0000125
textual definition: Inverse of developmentally induced by
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002258
has curation status: IAO_0000125
textual definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
editor note: false
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002260
textual definition: c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)

RO_0002261
textual definition: c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)

RO_0002262
textual definition: c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)

RO_0002263
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
textual definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.

RO_0002264
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
textual definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects

RO_0002285
has curation status: IAO_0000125
textual definition: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
editor note: This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: replaces

RO_0002286
has curation status: IAO_0000125
textual definition: Inverse of developmentally preceded by
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002287
example of usage: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
has curation status: IAO_0000125
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002291
has curation status: IAO_0000125
textual definition: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
editor note: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002292
has curation status: IAO_0000125
textual definition: y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002293
has curation status: IAO_0000125
textual definition: inverse of ubiquiotously expressed in
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002295
has curation status: IAO_0000125
textual definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
editor note: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002296
example of usage: every flower development (GO:0009908) results in development of some flower (PO:0009046)
has curation status: IAO_0000125
textual definition: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.geneontology.org/GO.doc.development.shtml

RO_0002297
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
example of usage: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
has curation status: IAO_0000125
term editor: https://orcid.org/0000-0002-6601-2165
definition source: GOC:mtg_berkeley_2013

RO_0002298
example of usage: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
example of usage: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
has curation status: IAO_0000125
textual definition: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: GOC:mtg_berkeley_2013

RO_0002299
example of usage: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
example of usage: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
has curation status: IAO_0000125
textual definition: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: GOC:mtg_berkeley_2013

RO_0002300
example of usage: foramen ovale closure SubClassOf results in disappearance of foramen ovale
has curation status: IAO_0000125
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002301
example of usage: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
has curation status: IAO_0000125
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002302
textual definition: Inverse of 'is substance that treats'

RO_0002303
example of usage: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
has curation status: IAO_0000428
textual definition: x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
term editor: https://orcid.org/0000-0002-4366-3088
alternative label: adapted for living in

RO_0002304
textual definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.

RO_0002305
textual definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.

RO_0002309
textual definition: A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.

RO_0002310
example of usage: An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes.
example of usage: An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
textual definition: OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
editor note: This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.

RO_0002313
textual definition: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: regulates localization of

RO_0002315
example of usage: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
textual definition: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
term editor: https://orcid.org/0000-0002-6601-2165
definition source: GOC:mtg_berkeley_2013

RO_0002320
textual definition: A relationship that holds via some environmental process
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002321
textual definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
editor note: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002322
editor note: An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: adapted for

RO_0002324
textual definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002325
example of usage: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
textual definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002326
example of usage: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
example of usage: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
example of usage: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
editor note: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002327
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
textual definition: c enables p iff c is capable of p and c acts to execute p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing

RO_0002328
textual definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002329
textual definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: false

RO_0002330
textual definition: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002331
textual definition: c involved_in p if and only if c enables some process p', and p' is part of p
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: actively involved in
alternative label: enables part of

RO_0002332
example of usage: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
textual definition: p regulates levels of c if p regulates some amount (PATO:0000070) of c
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002333
textual definition: inverse of enables
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002334
textual definition: inverse of regulates
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002335
textual definition: inverse of negatively regulates
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002336
textual definition: inverse of positively regulates
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002337
textual definition: A relationship that holds via some process of localization
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002338
textual definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002339
textual definition: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002340
textual definition: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002341
textual definition: Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002342
textual definition: Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002343
example of usage: 'pollen tube growth' results_in growth_of some 'pollen tube'
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002344
example of usage: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002345
textual definition: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002348
example of usage: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
textual definition: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002349
textual definition: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002350
example of usage: An organism that is a member of a population of organisms
textual definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO

RO_0002351
textual definition: has member is a mereological relation between a collection and an item.
definition source: SIO

RO_0002352
textual definition: inverse of has input
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002353
textual definition: inverse of has output
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002355
textual definition: A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002356
textual definition: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002357
textual definition: p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002371
textual definition: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002372
textual definition: m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Wikipedia:Insertion_(anatomy)

RO_0002373
textual definition: m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Wikipedia:Insertion_(anatomy)

RO_0002374
example of usage: false
has curation status: IAO_0000428
textual definition: x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
has_broad_synonym: has fused element

RO_0002375
has curation status: IAO_0000428
textual definition: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002376
example of usage: Deschutes River tributary_of Columbia River
example of usage: inferior epigastric vein tributary_of external iliac vein
has curation status: IAO_0000428
textual definition: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: drains into
alternative label: drains to
alternative label: tributary channel of
definition source: http://en.wikipedia.org/wiki/Tributary
definition source: http://www.medindia.net/glossary/venous_tributary.htm

RO_0002377
example of usage: Deschutes River distributary_of Little Lava Lake
has curation status: IAO_0000428
textual definition: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: branch of
alternative label: distributary channel of
definition source: http://en.wikipedia.org/wiki/Distributary

RO_0002378
has curation status: IAO_0000428
textual definition: x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: anastomoses with

RO_0002379
example of usage: A lump of clay and a statue
textual definition: x spatially_coextensive_with y if and inly if x and y have the same location
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002380
example of usage: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
textual definition: x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002381
example of usage: In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'.
has curation status: IAO_0000428
textual definition: x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002382
has curation status: IAO_0000428
textual definition: x proper_distributary_of y iff x distributary_of y and x does not flow back into y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002383
has curation status: IAO_0000428
textual definition: x proper_tributary_of y iff x tributary_of y and x does not originate from y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002384
has curation status: IAO_0000428
textual definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002385
has curation status: IAO_0000428
textual definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002386
has curation status: IAO_0000428
textual definition: x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002387
has curation status: IAO_0000428
textual definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002388
has curation status: IAO_0000428
textual definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002400
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
has curation status: IAO_0000428
textual definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: directly consumes

RO_0002402
example of usage: translation SubClassOf has_direct_output some protein
has curation status: IAO_0000428
textual definition: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: directly produces

RO_0002404
has curation status: IAO_0000428
textual definition: inverse of upstream of
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002407
textual definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly activates

RO_0002409
textual definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly inhibits

RO_0002410
textual definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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 yie…
term editor: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: RO_0002410
annotated property: textual definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
has db xref: https://en.wikipedia.org/wiki/Causality

RO_0002411
textual definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002412
textual definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002413
textual definition: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: directly provides input for
definition source: causal-relations

RO_0002414
has curation status: IAO_0000428
textual definition: transitive form of directly_provides_input_for
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002418
textual definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: influences (processual)
has_related_synonym: affects

RO_0002419
textual definition: An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.

RO_0002420
textual definition: A logical macro assertion whose domain is an IRI for a class
editor note: The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL

RO_0002424
editor note: false
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002427
textual definition: inverse of causally upstream of or within
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002428
textual definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002429
textual definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002430
textual definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002431
textual definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: involved in or reguates

RO_0002432
example of usage: A protein that enables activity in a cytosol.
textual definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: executes activity in
has_exact_synonym: enables activity in

Axiom
annotated source: RO_0002432
annotated property: textual definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: https://orcid.org/0000-0002-7073-9172

RO_0002433
textual definition: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002434
textual definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: Considering relabeling as 'pairwise interacts with'
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
term editor: https://orcid.org/0000-0002-6601-2165
has_exact_synonym: in pairwise interaction with

RO_0002435
editor note: An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002436
textual definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: binds
alternative label: molecularly binds with

RO_0002437
textual definition: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: interacts with on organism level

RO_0002438
textual definition: An interaction relationship in which the partners are related via a feeding relationship.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002439
example of usage: A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]
example of usage: Baleen whale preys on krill
textual definition: An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members
term editor: https://orcid.org/0000-0001-7134-3324
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-3138-4118
alternative label: is subject of predation interaction with
alternative label: preys upon

RO_0002440
textual definition: A biotic interaction in which the two organisms live together in more or less intimate association.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19278549

RO_0002441
textual definition: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19278549

RO_0002442
textual definition: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19278549

RO_0002443
textual definition: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/19278549

RO_0002444
example of usage: Pediculus humanus capitis parasite of human
textual definition: A parasite-host relationship where an organism benefits at the expense of another.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: parasitizes
has_exact_synonym: direct parasite of

RO_0002445
textual definition: Inverse of parasite of
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has parasite
alternative label: parasitised by
has_exact_synonym: directly parasitized by

RO_0002446
example of usage: Porifiera attaches to substrate
textual definition: A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.
term editor: https://orcid.org/0000-0002-6601-2165
has_related_synonym: semibiotically interacts with

RO_0002447
editor note: Axiomatization to GO to be added later
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

RO_0002448
textual definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
has_exact_synonym: molecularly controls

RO_0002449
textual definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly inhibits
has_exact_synonym: molecularly decreases activity of

RO_0002450
textual definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly activates
has_exact_synonym: molecularly increases activity of

RO_0002451
example of usage: all dengue disease transmitted by some mosquito
textual definition: A relationship that holds between a disease and organism
editor note: Add domain and range constraints
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002452
textual definition: A relation that holds between a disease or an organism and a phenotype
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002454
textual definition: X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002455
example of usage: Bees pollinate Flowers
editor note: This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: is subject of pollination interaction with

RO_0002456
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has polinator
alternative label: is target of pollination interaction with

RO_0002457
textual definition: Inverse of provides nutrients for
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002458
textual definition: inverse of preys on
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has predator
alternative label: is target of predation interaction with

RO_0002459
example of usage: Anopheles is a vector for Plasmodium
term editor: https://orcid.org/0000-0002-6601-2165
definition source: a is a vector for b if a carries and transmits an infectious pathogen b into another living organism

RO_0002469
textual definition: A biotic interaction where a material entity provides nutrition for an organism.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002470
textual definition: A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: is subject of eating interaction with

RO_0002471
textual definition: Inverse of eats
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: eaten by
alternative label: is target of eating interaction with

RO_0002472
textual definition: A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and the a supports either the existence of b, or the truth value of b.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002473
example of usage: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
textual definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552

RO_0002474
textual definition: An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.

RO_0002475
example of usage: 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'
textual definition: A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.
alternative label: shares no connection with

RO_0002476
example of usage: ABal nucleus child nucleus of ABa nucleus (in C elegans)
textual definition: c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002477
textual definition: A child nucleus relationship in which the cells are part of a hermaphroditic organism
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002478
textual definition: A child nucleus relationship in which the cells are part of a male organism
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002479
textual definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002480
textual definition: An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y
editor note: Axiomatization to GO to be added later
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002484
textual definition: Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)

RO_0002485
editor note: See notes for inverse relation
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002486
editor note: This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002488
textual definition: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002489
textual definition: x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002490
textual definition: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002491
textual definition: x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
term editor: https://orcid.org/0000-0002-6601-2165
has_exact_synonym: exists during

RO_0002492
textual definition: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002493
textual definition: x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002494
textual definition: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002495
textual definition: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002496
textual definition: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002497
textual definition: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002500
textual definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

RO_0002501
textual definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002503
textual definition: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
editor note: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

RO_0002504
example of usage: brain always_present_in_taxon 'Vertebrata'
example of usage: forelimb always_present_in_taxon Euarchontoglires
textual definition: S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S
editor note: This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed.
alternative label: never lost in

RO_0002505
example of usage: 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
textual definition: p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has intermediate product

RO_0002506
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002507
example of usage: A coral reef environment is determined by a particular coral reef
textual definition: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
editor note: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/24330602

RO_0002508
textual definition: inverse of determined by
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002509
textual definition: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002510
textual definition: x is transcribed from y if and only if x is synthesized from template y
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002511
textual definition: inverse of transcribed from
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002512
textual definition: x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002513
textual definition: inverse of ribosomal translation of
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002514
textual definition: A relation that holds between two entities that have the property of being sequences or having sequences.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002515
example of usage: Every UTR is adjacent to a CDS of the same transcript
example of usage: Two consecutive DNA residues are sequentially adjacent
example of usage: Two exons on a processed transcript that were previously connected by an intron are adjacent
textual definition: x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002516
example of usage: Every CDS has as a start sequence the start codon for that transcript
textual definition: x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: started by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002517
textual definition: inverse of has start sequence
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: starts
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002518
example of usage: Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)
textual definition: x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: ended by
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002519
textual definition: inverse of has end sequence
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: ends
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002520
textual definition: x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.
editor note: In the SO paper, this was defined as an instance-type relation
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002521
example of usage: Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence.
textual definition: x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002522
example of usage: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
textual definition: x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002523
textual definition: inverse of bounds sequence of
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002524
textual definition: x has subsequence y iff all of the sequence parts of y are sequence parts of x
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: contains
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

RO_0002525
textual definition: inverse of has subsequence
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: contained by

RO_0002526
textual definition: x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002527
textual definition: x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: disconnected from

RO_0002528
textual definition: inverse of downstream of sequence of
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002529
textual definition: x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002530
example of usage: A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript
textual definition: x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002531
example of usage: A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript
textual definition: inverse of immediately downstream of
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002532
textual definition: Any entity that is ordered in discrete units along a linear axis.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002533
textual definition: Any individual unit of a collection of like units arranged in a linear order
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002534
textual definition: Any entity that can be divided into parts such that each part is an atomical unit of a sequence
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002539
textual definition: Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.

RO_0002540
textual definition: Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.

RO_0002541
textual definition: Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.

RO_0002542
textual definition: Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2

RO_0002543
textual definition: Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.

RO_0002544
textual definition: Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2

RO_0002545
textual definition: Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.

RO_0002546
textual definition: A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process

RO_0002547
textual definition: Count of number of days intervening between the start of the stage and the time of coitum.

RO_0002548
textual definition: Count of number of days intervening between the end of the stage and the time of coitum.

RO_0002551
example of usage: Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
textual definition: A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has supporting framework

RO_0002552
textual definition: p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002553
textual definition: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
editor note: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://eol.org/schema/terms/hyperparasitoidOf
definition source: https://en.wikipedia.org/wiki/Hyperparasite
has_narrow_synonym: hyperparasitoid of
has_related_synonym: epiparasite of

RO_0002554
textual definition: inverse of hyperparasite of
term editor: https://orcid.org/0000-0002-6601-2165
has_related_synonym: has epiparasite
has_related_synonym: has hyperparasite
has_related_synonym: hyperparasitoidized by

RO_0002556
textual definition: Inverse of has pathogen
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002557
textual definition: A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002558
textual definition: inverse of is evidence for
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/25052702

RO_0002560
textual definition: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p

RO_0002561
textual definition: If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p

RO_0002562
textual definition: R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process

RO_0002565
textual definition: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002566
textual definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
definition source: causal-relations

RO_0002567
textual definition: A relation that holds between elements of a musculoskeletal system or its analogs.
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002568
textual definition: m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Wikipedia:Antagonist_(muscle)

RO_0002569
textual definition: inverse of branching part of
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002570
textual definition: x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: UBERON:cjm

RO_0002571
textual definition: x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: https://orcid.org/0000-0002-6601-2165

RO_0002572
textual definition: s is luminal space of x iff s is lumen_of x and s is an immaterial entity
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002573
textual definition: A relation that holds between an attribute or a qualifier and another attribute.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

RO_0002575
textual definition: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
editor note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"

RO_0002576
textual definition: inverse of has skeleton
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002578
textual definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002579
textual definition: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y

RO_0002581
textual definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

RO_0002582
textual definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

RO_0002583
textual definition: holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).

RO_0002584
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
textual definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
term editor: https://orcid.org/0000-0002-6601-2165

RO_0002585
editor note: p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.

RO_0002586
textual definition: p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p

RO_0002589
textual definition: p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.

RO_0002592
textual definition: p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c

RO_0002593
textual definition: holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).

RO_0002594
textual definition: An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.

RO_0002595
textual definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

RO_0002596
example of usage: pyrethroid -> growth
textual definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

RO_0002597
textual definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

RO_0002598
example of usage: renin -> arteriolar smooth muscle contraction
textual definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

RO_0002599
example of usage: pazopanib -> pathological angiogenesis
textual definition: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
alternative label: treats
definition source: causal-relations

Axiom
annotated source: RO_0002599
annotated property: alternative label
annotated target: treats
comment: Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship

RO_0002600
example of usage: benzene -> cancer [CHEBI]
textual definition: Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
alternative label: causes disease
definition source: causal-relations

RO_0002601
textual definition: A shortcut relationship that holds between two entities based on their identity criteria

RO_0002602
textual definition: A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.

RO_0002603
textual definition: x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y

RO_0002604
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: 'increase in temperature' is-opposite-of 'decrease in temperature'
textual definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).

RO_0002605
textual definition: x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).

RO_0002606
textual definition: c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
alternative label: treats
definition source: causal-relations

RO_0002607
textual definition: c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
editor note: May be ceded to OBI

RO_0002608
textual definition: Inverse of 'causal agent in process'
definition source: causal-relations

RO_0002609
textual definition: A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.

RO_0002610
textual definition: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.

RO_0002612
textual definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom

RO_0002613
textual definition: A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom

RO_0002614
example of usage: An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support.
textual definition: A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.

RO_0002615
textual definition: Inverse of is-model-of

RO_0002617
example of usage: In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context.
textual definition: this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.

RO_0002629
textual definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
definition source: causal-relations

RO_0002630
textual definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
definition source: causal-relations

RO_0002632
textual definition: A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host
definition source: Types

RO_0002633
textual definition: inverse of ectoparasite of

RO_0002634
definition source: Types
definition source: A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system
has_related_synonym: lives inside of

RO_0002636
textual definition: A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite

RO_0002637
textual definition: inverse of mesoparasite of

RO_0002638
textual definition: A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
definition source: Types

RO_0002639
textual definition: inverse of intercellular endoparasite of

RO_0002640
textual definition: A sub-relation of endoparasite-of in which the parasite inhabits host cells.
definition source: Types

RO_0002641
textual definition: inverse of intracellular endoparasite of

RO_0002801
textual definition: Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting.
definition source: Communal roosting

RO_0002802
example of usage: An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s.
textual definition: A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host.
definition source: v13071356

RO_0002803
example of usage: An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s.
textual definition: inverse of reservoir host of

RO_0003000
has curation status: IAO_0000125
textual definition: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
term editor: https://orcid.org/0000-0001-9114-8737

RO_0003001
has curation status: IAO_0000125
textual definition: a produced_by b iff some process that occurs_in b has_output a.
term editor: https://orcid.org/0000-0001-9114-8737

RO_0003002
textual definition: Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0003003
textual definition: Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0003301
textual definition: A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
term editor: https://orcid.org/0000-0002-1048-5019
alternative label: is used to study

RO_0003302
example of usage: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
textual definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
editor note: Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.

RO_0003303
textual definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.

RO_0003304
textual definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.

RO_0003305
textual definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
alternative label: contributes to expressivity of condition

RO_0003306
textual definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
alternative label: contributes to penetrance of condition

RO_0003307
textual definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
alternative label: is preventative for condition

RO_0003308
textual definition: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

RO_0003309
textual definition: A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.

RO_0003310
textual definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.

RO_0003311
textual definition: A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.

RO_0004007
textual definition: p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.

RO_0004008
textual definition: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.

Axiom
annotated source: RO_0004008
annotated property: textual definition
annotated target: p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: GOC:dph
has db xref: GOC:kva
has db xref: GOC:pt
comment: PMID:27812932

RO_0004009
textual definition: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.

Axiom
annotated source: RO_0004009
annotated property: textual definition
annotated target: p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: GOC:dph
has db xref: GOC:kva
has db xref: GOC:pt
comment: PMID:27812932

RO_0004011
textual definition: Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].

RO_0004012
textual definition: Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].

RO_0004013
textual definition: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].

RO_0004014
textual definition: Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].

RO_0004015
textual definition: Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].

RO_0004016
textual definition: Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].

RO_0004020
textual definition: A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.

RO_0004021
textual definition: A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.

RO_0004022
textual definition: A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.

RO_0004024
textual definition: A relationship between a disease and a process where the disease process disrupts the execution of the process.

RO_0004026
textual definition: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
editor note: TODO: complete range axiom once more of CARO has been mireoted in to this ontology

RO_0004027
textual definition: A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity

RO_0004028
textual definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.

RO_0004029
textual definition: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.

RO_0004030
textual definition: A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.

RO_0004031
textual definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.

RO_0004034
textual definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive

RO_0004035
textual definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative

RO_0004036
textual definition: true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.

RO_0004048
textual definition: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"

RO_0007000
textual definition: A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.

RO_0007001
textual definition: A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.

RO_0008501
textual definition: An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
definition source: https://en.wikipedia.org/wiki/Epiphyte

RO_0008502
textual definition: inverse of epiphyte of

RO_0008503
textual definition: A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material
definition source: https://en.wikipedia.org/wiki/Kleptoparasitism

RO_0008504
textual definition: inverse of kleptoparasite of

RO_0008505
textual definition: An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.

RO_0008506
textual definition: An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.

RO_0008507
textual definition: An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.

RO_0008508
textual definition: inverse of lays eggs on

RO_0008509
example of usage: Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)
textual definition: x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.

RO_0009001
example of usage: muffin 'has substance added' some 'baking soda'
has curation status: IAO_0000428
textual definition: "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
editor note: The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
term editor: https://orcid.org/0000-0002-8844-9165

RO_0009002
example of usage: 'egg white' 'has substance removed' some 'egg yolk'
has curation status: IAO_0000428
textual definition: "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.
term editor: https://orcid.org/0000-0002-8844-9165

RO_0009003
example of usage: sardines 'immersed in' some 'oil and mustard'
has curation status: IAO_0000428
textual definition: "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.
term editor: https://orcid.org/0000-0002-8844-9165

RO_0009004
example of usage: sardine has consumer some homo sapiens
has curation status: IAO_0000428
textual definition: 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.
term editor: https://orcid.org/0000-0002-8844-9165

RO_0009005
example of usage: bread 'has primary substance added' some 'flour'
has curation status: IAO_0000428
textual definition: 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.
term editor: https://orcid.org/0000-0002-8844-9165

RO_0009006
example of usage: A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material.
textual definition: A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic.

RO_0009007
textual definition: Inverse of 'assay measures characteristic'

RO_0009501
example of usage: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
example of usage: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
example of usage: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
textual definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
has_exact_synonym: triggered by process

Axiom
annotated source: RO_0009501
annotated property: has_exact_synonym
annotated target: triggered by process
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0010001
example of usage: Genetic information generically depend on molecules of DNA.
example of usage: The novel *War and Peace* generically depends on this copy of the novel.
example of usage: The pattern shared by chess boards generically depends on any chess board.
example of usage: The score of a symphony g-depends on a copy of the score.
example of usage: This pdf file generically depends on this server.
textual definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
definition source: [072-ISO]
has_exact_synonym: g-depends on

RO_0010002
example of usage: Molecules of DNA are carriers of genetic information.
example of usage: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
example of usage: This hard drive is carrier of these data items.
textual definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
definition source: [072-ISO]

RO_0011002
textual definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011003
textual definition: The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011004
textual definition: The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011007
textual definition: The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011008
textual definition: The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011009
textual definition: The entity A has an activity that directly positively regulates the quantity of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011010
textual definition: The entity A has an activity that directly negatively regulates the quantity of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011013
textual definition: The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: indirectly activates

RO_0011014
example of usage: AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
textual definition: An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011015
example of usage: AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
textual definition: An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011016
textual definition: The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: indirectly inhibits

RO_0011021
textual definition: The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011022
textual definition: The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011023
textual definition: The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0011024
textual definition: The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
term editor: https://orcid.org/0000-0003-4639-4431

RO_0012000
textual definition: a relation between a process and a continuant, in which the process is regulated by the small molecule continuant

RO_0012001
textual definition: a relation between a process and a continuant, in which the process is activated by the small molecule continuant

RO_0012002
textual definition: a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant

RO_0012003
textual definition: p acts on population of c iff c' is a collection, has members of type c, and p has participant c

RO_0012004
textual definition: a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process

RO_0012005
textual definition: a relation between a continuant and a process, in which the continuant is a small molecule that activates the process

RO_0012006
textual definition: a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process

RO_0012007
textual definition: The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.

RO_0012009
textual definition: p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.

RO_0012010
textual definition: p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.

RO_0012011
textual definition: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.

RO_0012012
textual definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.

RO_0012013
textual definition: x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
has_exact_synonym: positively regulates in other organism

RO_0012014
textual definition: x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
has_exact_synonym: negatively regulates in other organism

RO_0013001
textual definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
has_exact_synonym: has synaptic input or output in

RO_0013002
textual definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.

RO_0013003
textual definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.

RO_0013004
textual definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).

RO_0013005
textual definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).

RO_0013006
textual definition: A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).

RO_0013007
textual definition: Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.
has_exact_synonym: has sensory dendrite location
has_exact_synonym: has sensory terminal in
has_exact_synonym: has sensory terminal location

RO_0013008
textual definition: A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.

RO_0013009
textual definition: A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.

RO_0014001
textual definition: A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.

RO_0015001
example of usage: transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])
textual definition: A relation between a material entity and some data in which the data is taken as exemplifying the material entity.
editor note: C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C.
term editor: https://orcid.org/0000-0002-5260-9315

RO_0015003
textual definition: A relation between a group and another group it is part of but does not fully constitute.
editor note: X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y.
term editor: https://orcid.org/0000-0001-7258-9596

RO_0015004
example of usage: 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1').
example of usage: transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3.
textual definition: A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.
editor note: C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.
has_exact_synonym: has marker gene combination
has_exact_synonym: has marker signature set

RO_0015006
textual definition: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: RO_0015006
annotated property: textual definition
annotated target: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0015007
textual definition: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: RO_0015007
annotated property: textual definition
annotated target: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0015008
textual definition: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: RO_0015008
annotated property: textual definition
annotated target: q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0015009
textual definition: q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: RO_0015009
annotated property: textual definition
annotated target: q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0015011
textual definition: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.

Axiom
annotated source: RO_0015011
annotated property: textual definition
annotated target: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0015012
textual definition: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.

Axiom
annotated source: RO_0015012
annotated property: textual definition
annotated target: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
has db xref: https://orcid.org/0000-0002-6601-2165

RO_0015015
example of usage: 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
textual definition: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.

Axiom
annotated source: RO_0015015
annotated property: textual definition
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
has db xref: PMID:19243617

RO_0015016
example of usage: 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
textual definition: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.

Axiom
annotated source: RO_0015016
annotated property: textual definition
annotated target: A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
has db xref: PMID:19243617

RO_0016002
textual definition: A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.

RO_0016004
textual definition: X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.
definition source: ExO:0000083

RO_0017001
example of usage: A diagnostic testing device utilizes a specimen.
textual definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
has_broad_synonym: utilizes

RO_0017003
textual definition: A relation between entities in which one increases or decreases as the other does the same.
alternative label: directly correlated with

RO_0017004
textual definition: A relation between entities in which one increases as the other decreases.
alternative label: inversely correlated with

RO_0017005
example of usage: anticoagulant-containing test tube contains measured amount 5 ml of blood specimen.
textual definition: A relation between a container and measurement datum that specifies the actual amount of material in the container.

RO_0017006
example of usage: anticoagulant-containing test tube has maximum capacity 10 ml.
textual definition: A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume.

RO_0017008
example of usage: biobank organization owns a specimen
example of usage: hospital owns a laboratory facility
textual definition: A primitive relation that holds between entities x and y in which y is at x's full disposal.

RO_0017009
example of usage: freezer is owned by a biobank organization
textual definition: Inverse of the owns relation.

RO_0018001
textual definition: Helper relation for OWL definition of RO:0018002 myristoylates

RO_0018002
textual definition: A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input

RO_0018003
textual definition: inverse of myristoylates

RO_0018027
example of usage: mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)
textual definition: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor

RO_0018028
example of usage: pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)
textual definition: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level

RO_0018029
example of usage: tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)
textual definition: a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level

RO_0018031
example of usage: pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816)
textual definition: A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B.

RO_0018032
example of usage: neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361)
textual definition: A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B.

RO_0018033
example of usage: (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons.
textual definition: A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.

RO_0018034
example of usage: (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons.
textual definition: A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations.

RO_0018035
example of usage: phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol.
textual definition: A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
has_exact_synonym: is MMP with
has_exact_synonym: is matched molecular pair with

Axiom
annotated source: RO_0018035
annotated property: textual definition
annotated target: A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C.
source: ddr.21045
source: jm200452d
source: Matched molecular pair analysis

RO_0018036
example of usage: 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.
textual definition: Two chemicals are tautomers if they can be readily interconverted. This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
has_exact_synonym: is desmotrope of

Axiom
annotated source: RO_0018036
annotated property: example of usage
annotated target: 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol.

RO_0018037
example of usage: carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)
textual definition: Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization.

Axiom
annotated source: RO_0018037
annotated property: example of usage
annotated target: carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795)

RO_0018038
example of usage: hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)
textual definition: Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.

Axiom
annotated source: RO_0018038
annotated property: example of usage
annotated target: hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851)

RO_0018039
example of usage: dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
textual definition: Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
has_exact_synonym: is optical isomer of

Axiom
annotated source: RO_0018039
annotated property: example of usage
annotated target: dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped.
comment: CHEBI_48557

RO_0018040
example of usage: pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.
textual definition: Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B.

Axiom
annotated source: RO_0018040
annotated property: example of usage
annotated target: pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates.

RO_0019000
textual definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.

RO_0019001
textual definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.

RO_0019002
textual definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.

RO_0019501
textual definition: Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.

RO_0020101
example of usage: brachial artery vessel supplies blood to brachialis muscle
textual definition: x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y.

RO_0020102
example of usage: cystic vein vessel drains blood from gallbladder
textual definition: x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y.

RO_0020103
example of usage: alveolar capillary directly supplies and drains some alveolus
textual definition: x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y.

RO_0020202
textual definition: A relationship between a ratio or proportion and its dividend.
has_exact_synonym: has dividend

RO_0020203
textual definition: A relationship between a ratio or proportion and its divisor.
has_exact_synonym: has divisor

RO_0040035
textual definition: This relation groups relations between diseases and any other kind of entity.

RO_0040036
textual definition: p has anatomical participant c iff p has participant c, and c is an anatomical entity

RO_0040042
example of usage: part-of is homeomorphic for independent continuants.
textual definition: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.

RO HOM0000000
textual definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
editor note: TODO: Add homeomorphy axiom
has_exact_synonym: sameness
has_exact_synonym: similar to
has_related_synonym: correspondence
has_related_synonym: resemblance

Axiom
annotated source: RO HOM0000000
annotated property: textual definition
annotated target: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
has db xref: HOM_0000000
has db xref: BGEE:curator

Axiom
annotated source: RO HOM0000000
annotated property: has_related_synonym
annotated target: correspondence
has db xref: http://dx.doi.org/10.1007/BF02814479

RO HOM0000001
textual definition: Similarity that results from common evolutionary origin.
has_exact_synonym: homologous to

Axiom
annotated source: RO HOM0000001
annotated property: textual definition
annotated target: Similarity that results from common evolutionary origin.
has db xref: bies.950180611
has db xref: jmor.1051730307
has db xref: http://dx.doi.org/10.1007/BF02814480
has db xref: HOM_0000001

RO HOM0000002
textual definition: Similarity that results from independent evolution.
has_exact_synonym: homoplasous to
has_related_synonym: analogy

Axiom
annotated source: RO HOM0000002
annotated property: textual definition
annotated target: Similarity that results from independent evolution.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000002

RO HOM0000003
textual definition: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
has_exact_synonym: homocracous to

Axiom
annotated source: RO HOM0000003
annotated property: textual definition
annotated target: Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: s00427-003-0301-4
has db xref: http://dx.doi.org/10.1186/1742-9994-2-15
has db xref: HOM_0000003

RO HOM0000004
textual definition: Homoplasy that involves different underlying mechanisms or structures.
has_related_synonym: analogy

Axiom
annotated source: RO HOM0000004
annotated property: textual definition
annotated target: Homoplasy that involves different underlying mechanisms or structures.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000004

RO HOM0000005
textual definition: Homoplasy that involves homologous underlying mechanisms or structures.
has_exact_synonym: parallel evolution

Axiom
annotated source: RO HOM0000005
annotated property: textual definition
annotated target: Homoplasy that involves homologous underlying mechanisms or structures.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000005

RO HOM0000006
textual definition: Homology that is defined by similarity with regard to selected structural parameters.
has_exact_synonym: structural homologous to
has_related_synonym: idealistic homology

Axiom
annotated source: RO HOM0000006
annotated property: textual definition
annotated target: Homology that is defined by similarity with regard to selected structural parameters.
has db xref: j.jhevol.2006.11.014
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000006
has db xref: ISBN:0123195837

RO HOM0000007
textual definition: Homology that is defined by common descent.
has_broad_synonym: homology
has_exact_synonym: cladistic homology
has_exact_synonym: historical homologous to
has_exact_synonym: phylogenetic homology
has_exact_synonym: taxic homology
has_related_synonym: true homology

Axiom
annotated source: RO HOM0000007
annotated property: textual definition
annotated target: Homology that is defined by common descent.
has db xref: S0169-5347(97)01125-7
has db xref: HOM_0000007
has db xref: ISBN:0123195837

RO HOM0000008
textual definition: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
has_exact_synonym: biological homologous to
has_related_synonym: transformational homology

Axiom
annotated source: RO HOM0000008
annotated property: textual definition
annotated target: Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype.
has db xref: S0169-5347(97)01125-7
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000008

RO HOM0000009
textual definition: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
has_exact_synonym: atavism
has_exact_synonym: rudiment
has_related_synonym: reversion

Axiom
annotated source: RO HOM0000009
annotated property: textual definition
annotated target: Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage.
has db xref: j.jhevol.2006.11.010
has db xref: HOM_0000009

RO HOM0000010
textual definition: Structural homology that is detected by similarity in content and organization between chromosomes.
has_exact_synonym: syntenic homologous to
has_related_synonym: synteny

Axiom
annotated source: RO HOM0000010
annotated property: textual definition
annotated target: Structural homology that is detected by similarity in content and organization between chromosomes.
has db xref: HOM_0000010
has db xref: MeSH:Synteny

RO HOM0000011
textual definition: Historical homology that involves genes that diverged after a duplication event.
has_exact_synonym: paralogous to

Axiom
annotated source: RO HOM0000011
annotated property: textual definition
annotated target: Historical homology that involves genes that diverged after a duplication event.
has db xref: S0168-9525(00)02005-9
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000011
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/5449325

RO HOM0000012
textual definition: Paralogy that involves sets of syntenic blocks.
has_exact_synonym: syntenic paralogous to
has_related_synonym: duplicon
has_related_synonym: paralogon

Axiom
annotated source: RO HOM0000012
annotated property: textual definition
annotated target: Paralogy that involves sets of syntenic blocks.
has db xref: 1471-213X-7-100
has db xref: HOM_0000012
has db xref: DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y

RO HOM0000013
textual definition: Syntenic homology that involves chromosomes of different species.
has_exact_synonym: syntenic orthologous to

Axiom
annotated source: RO HOM0000013
annotated property: textual definition
annotated target: Syntenic homology that involves chromosomes of different species.
has db xref: gr.6380007
has db xref: HOM_0000013

RO HOM0000014
textual definition: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
has_exact_synonym: fractional homology
has_exact_synonym: partial homologous to
has_exact_synonym: segmental homology
has_related_synonym: mixed homology
has_related_synonym: modular homology
has_related_synonym: partial correspondence
has_related_synonym: percent homology

Axiom
annotated source: RO HOM0000014
annotated property: textual definition
annotated target: Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.
has db xref: HOM_0000014
has db xref: ISBN:0123195837
has db xref: ISBN:978-0471984931

RO HOM0000015
textual definition: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
has_exact_synonym: protein structural homologous to

Axiom
annotated source: RO HOM0000015
annotated property: textual definition
annotated target: Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence.
has db xref: 0022-2836(76)90195-9
has db xref: HOM_0000015

RO HOM0000016
textual definition: Structural homology that involves a pseudogenic feature and its functional ancestor.
has_broad_synonym: pseudogene
has_exact_synonym: non functional homologous to

Axiom
annotated source: RO HOM0000016
annotated property: textual definition
annotated target: Structural homology that involves a pseudogenic feature and its functional ancestor.
has db xref: HOM_0000016
has db xref: SO:non_functional_homolog_of

RO HOM0000017
textual definition: Historical homology that involves genes that diverged after a speciation event.
has_exact_synonym: orthologous to

Axiom
annotated source: RO HOM0000017
annotated property: textual definition
annotated target: Historical homology that involves genes that diverged after a speciation event.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: S0168-9525(00)02005-9
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000017
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/5449325

RO HOM0000018
textual definition: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
has_exact_synonym: xenologous to

Axiom
annotated source: RO HOM0000018
annotated property: textual definition
annotated target: Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor.
has db xref: S0168-9525(00)02005-9
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000018

RO HOM0000019
textual definition: Historical homology that involves two members sharing no other homologs in the lineages considered.
has_exact_synonym: 1 to 1 homologous to
has_exact_synonym: 1:1 homology
has_exact_synonym: one-to-one homology

Axiom
annotated source: RO HOM0000019
annotated property: textual definition
annotated target: Historical homology that involves two members sharing no other homologs in the lineages considered.
has db xref: HOM_0000019
has db xref: BGEE:curator

RO HOM0000020
textual definition: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
has_exact_synonym: 1 to 1 orthologous to
has_exact_synonym: 1:1 orthology
has_exact_synonym: one-to-one orthology

Axiom
annotated source: RO HOM0000020
annotated property: textual definition
annotated target: Orthology that involves two genes that did not experience any duplication after the speciation event that created them.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: HOM_0000020
has db xref: homology method.html

RO HOM0000022
textual definition: Paralogy that results from a whole genome duplication event.
has_exact_synonym: ohnologous to
has_related_synonym: homoeology

Axiom
annotated source: RO HOM0000022
annotated property: textual definition
annotated target: Paralogy that results from a whole genome duplication event.
has db xref: http://dx.doi.org/10.1038/75560
has db xref: HOM_0000022

RO HOM0000023
textual definition: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
has_exact_synonym: in-paralogous to
has_exact_synonym: inparalogy
has_exact_synonym: symparalogy

Axiom
annotated source: RO HOM0000023
annotated property: textual definition
annotated target: Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000023

RO HOM0000024
textual definition: Paralogy that results from a duplication preceding a given speciation event.
has_exact_synonym: alloparalogy
has_exact_synonym: out-paralogous to
has_exact_synonym: outparalogy

Axiom
annotated source: RO HOM0000024
annotated property: textual definition
annotated target: Paralogy that results from a duplication preceding a given speciation event.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000024

RO HOM0000025
textual definition: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
has_exact_synonym: pro-orthologous to

Axiom
annotated source: RO HOM0000025
annotated property: textual definition
annotated target: 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.
has db xref: scdb.1999.0338
has db xref: nrg2099
has db xref: HOM_0000025

RO HOM0000026
textual definition: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
has_exact_synonym: semi-orthologous to

Axiom
annotated source: RO HOM0000026
annotated property: textual definition
annotated target: 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.
has db xref: scdb.1999.0338
has db xref: nrg2099
has db xref: HOM_0000026

RO HOM0000027
textual definition: Iterative homology that involves structures arranged along the main body axis.
has_exact_synonym: serial homologous to
has_related_synonym: homonomy

Axiom
annotated source: RO HOM0000027
annotated property: textual definition
annotated target: Iterative homology that involves structures arranged along the main body axis.
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000027

RO HOM0000028
textual definition: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
has_exact_synonym: heterochronous homologous to
has_exact_synonym: heterochrony

Axiom
annotated source: RO HOM0000028
annotated property: textual definition
annotated target: Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.
has db xref: HOM_0000028
has db xref: ISBN:978-0674639416

RO HOM0000029
textual definition: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
has_exact_synonym: juvenification
has_exact_synonym: pedomorphosis

Axiom
annotated source: RO HOM0000029
annotated property: textual definition
annotated target: Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.
has db xref: Pedomorphosis
has db xref: HOM_0000029
has db xref: ISBN:978-0674639416

RO HOM0000030
textual definition: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.

Axiom
annotated source: RO HOM0000030
annotated property: textual definition
annotated target: Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.
has db xref: Peramorphosis
has db xref: HOM_0000030

RO HOM0000031
textual definition: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.

Axiom
annotated source: RO HOM0000031
annotated property: textual definition
annotated target: Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.
has db xref: Progenesis
has db xref: HOM_0000031
has db xref: ISBN:978-0674639416

RO HOM0000032
textual definition: Paedomorphosis that is produced by a retardation of somatic development.
has_exact_synonym: juvenilization
has_exact_synonym: neotenous to

Axiom
annotated source: RO HOM0000032
annotated property: textual definition
annotated target: Paedomorphosis that is produced by a retardation of somatic development.
has db xref: Neoteny
has db xref: HOM_0000032
has db xref: ISBN:978-0674639416

RO HOM0000033
textual definition: Convergence that results from co-evolution usually involving an evolutionary arms race.
has_exact_synonym: mimicrous to

Axiom
annotated source: RO HOM0000033
annotated property: textual definition
annotated target: Convergence that results from co-evolution usually involving an evolutionary arms race.
has db xref: Mimicry
has db xref: HOM_0000033

RO HOM0000034
textual definition: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
has_exact_synonym: 1 to many orthologous to
has_exact_synonym: 1:many orthology
has_exact_synonym: one-to-many orthology
has_related_synonym: co-orthology
has_related_synonym: many to 1 orthology

Axiom
annotated source: RO HOM0000034
annotated property: textual definition
annotated target: Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.
has db xref: 415741a
has db xref: HOM_0000034
has db xref: homology method.html

RO HOM0000036
textual definition: Historical homology that involves two members of a larger set of homologs.
has_exact_synonym: many to many homologous to
has_exact_synonym: many-to-many homology
has_exact_synonym: many:many homology

Axiom
annotated source: RO HOM0000036
annotated property: textual definition
annotated target: Historical homology that involves two members of a larger set of homologs.
has db xref: msp002
has db xref: HOM_0000036

RO HOM0000037
textual definition: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
has_exact_synonym: 1 to many homologous to
has_exact_synonym: one-to-many homology
has_related_synonym: 1:many homology

Axiom
annotated source: RO HOM0000037
annotated property: textual definition
annotated target: Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.
has db xref: HOM_0000037
has db xref: BGEE:curator

RO HOM0000042
textual definition: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
has_exact_synonym: apomorphous to
has_related_synonym: synapomorphy

Axiom
annotated source: RO HOM0000042
annotated property: textual definition
annotated target: Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.
has db xref: HOM_0000042
has db xref: ISBN:978-0252068140

RO HOM0000043
textual definition: Historical homology that is based on distant shared ancestry.
has_exact_synonym: plesiomorphous to
has_related_synonym: symplesiomorphy

Axiom
annotated source: RO HOM0000043
annotated property: textual definition
annotated target: Historical homology that is based on distant shared ancestry.
has db xref: HOM_0000043
has db xref: ISBN:978-0252068140

RO HOM0000044
textual definition: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
has_exact_synonym: deep genetic homology
has_exact_synonym: deep homologous to
has_related_synonym: generative homology
has_related_synonym: homoiology

Axiom
annotated source: RO HOM0000044
annotated property: textual definition
annotated target: Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: nature07891
has db xref: HOM_0000044

RO HOM0000045
textual definition: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
has_exact_synonym: hemiplasous to

Axiom
annotated source: RO HOM0000045
annotated property: textual definition
annotated target: Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.
has db xref: pnas.0807433105
has db xref: HOM_0000045

RO HOM0000046
textual definition: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
has_exact_synonym: gametologous to

Axiom
annotated source: RO HOM0000046
annotated property: textual definition
annotated target: Historical homology that involves not recombining and subsequently differentiated sex chromosomes.
has db xref: HOM_0000046
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/11110898

RO HOM0000047
textual definition: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
has_exact_synonym: chromosomal homologous to

Axiom
annotated source: RO HOM0000047
annotated property: textual definition
annotated target: Historical homology that involves the chromosomes able to pair (synapse) during meiosis.
has db xref: HOM_0000047
has db xref: ISBN:0195307615

RO HOM0000048
textual definition: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
has_exact_synonym: many to many orthologous to
has_exact_synonym: many-to-many orthology
has_exact_synonym: many:many orthology
has_exact_synonym: trans-orthology
has_related_synonym: co-orthology
has_related_synonym: trans-homology

Axiom
annotated source: RO HOM0000048
annotated property: textual definition
annotated target: Orthology that involves two genes that experienced duplications more recent than the species split that created them.
has db xref: 415741a
has db xref: HOM_0000048
has db xref: homology method.html

RO HOM0000049
textual definition: Paralogy that involves genes from the same species.
has_exact_synonym: within-species paralogous to

Axiom
annotated source: RO HOM0000049
annotated property: textual definition
annotated target: Paralogy that involves genes from the same species.
has db xref: HOM_0000049
has db xref: homology method.html

RO HOM0000050
textual definition: Paralogy that involves genes from different species.
has_exact_synonym: between-species paralogous to

Axiom
annotated source: RO HOM0000050
annotated property: textual definition
annotated target: Paralogy that involves genes from different species.
has db xref: HOM_0000050
has db xref: homology method.html

RO HOM0000051
textual definition: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
has_exact_synonym: post-displacement

Axiom
annotated source: RO HOM0000051
annotated property: textual definition
annotated target: Paedomorphosis that is produced by delayed growth of immature structures into the adult form.
has db xref: Pedomorphosis
has db xref: HOM_0000051

RO HOM0000052
textual definition: Peramorphosis that is produced by a delay in the offset of development.

Axiom
annotated source: RO HOM0000052
annotated property: textual definition
annotated target: Peramorphosis that is produced by a delay in the offset of development.
has db xref: Peramorphosis
has db xref: HOM_0000052
has db xref: ISBN:978-0674639416

RO HOM0000053
textual definition: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
has_exact_synonym: synologous to

Axiom
annotated source: RO HOM0000053
annotated property: textual definition
annotated target: Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.
has db xref: http://dx.doi.org/10.1007/BF00173425
has db xref: S0168-9525(00)02005-9
has db xref: HOM_0000053

RO HOM0000054
textual definition: Orthology that involves functional equivalent genes with retention of the ancestral function.
has_exact_synonym: isoorthologous to

Axiom
annotated source: RO HOM0000054
annotated property: textual definition
annotated target: Orthology that involves functional equivalent genes with retention of the ancestral function.
has db xref: S0168-9525(00)02005-9
has db xref: HOM_0000054

RO HOM0000055
textual definition: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
has_exact_synonym: tandem paralogous to
has_related_synonym: iterative paralogy
has_related_synonym: serial paralogy

Axiom
annotated source: RO HOM0000055
annotated property: textual definition
annotated target: Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.
has db xref: S0168-9525(00)02005-9
has db xref: HOM_0000055
has db xref: ISBN:978-0878932665

RO HOM0000057
textual definition: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
has_exact_synonym: apomorphic tendency
has_exact_synonym: cryptic homology
has_exact_synonym: latent homologous to
has_exact_synonym: underlying synapomorphy
has_related_synonym: homoiology
has_related_synonym: homoplastic tendency
has_related_synonym: re-awakening

Axiom
annotated source: RO HOM0000057
annotated property: textual definition
annotated target: Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: j.jhevol.2006.11.010
has db xref: http://dx.doi.org/10.1186/1742-9994-2-15
has db xref: HOM_0000057
has db xref: ISBN:0199141118

RO HOM0000058
textual definition: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
has_exact_synonym: generative homology
has_exact_synonym: syngenous to

Axiom
annotated source: RO HOM0000058
annotated property: textual definition
annotated target: Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.
has db xref: http://dx.doi.org/10.1186/1742-9994-2-15
has db xref: HOM_0000058
has db xref: DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R

RO HOM0000060
textual definition: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
has_exact_synonym: 1:1 paralogy
has_exact_synonym: apparent 1:1 orthology
has_exact_synonym: apparent orthologous to
has_exact_synonym: pseudoorthology

Axiom
annotated source: RO HOM0000060
annotated property: textual definition
annotated target: Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000060
has db xref: homology method.html

RO HOM0000061
textual definition: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
has_exact_synonym: pseudoparalogous to

Axiom
annotated source: RO HOM0000061
annotated property: textual definition
annotated target: Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.
has db xref: annurev.genet.39.073003.114725
has db xref: HOM_0000061

RO HOM0000062
textual definition: Historical homology that involves functional equivalent genes with retention of the ancestral function.
has_exact_synonym: equivalogous to

Axiom
annotated source: RO HOM0000062
annotated property: textual definition
annotated target: Historical homology that involves functional equivalent genes with retention of the ancestral function.
has db xref: gkl1043
has db xref: HOM_0000062

RO HOM0000063
textual definition: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
has_exact_synonym: interologous to

Axiom
annotated source: RO HOM0000063
annotated property: textual definition
annotated target: Historical homology that involves orthologous pairs of interacting molecules in different organisms.
has db xref: gr.1774904
has db xref: science.287.5450.116
has db xref: HOM_0000063

RO HOM0000065
textual definition: Similarity that is characterized by interchangeability in function.
has_related_synonym: functional similarity

Axiom
annotated source: RO HOM0000065
annotated property: textual definition
annotated target: Similarity that is characterized by interchangeability in function.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: 415741a
has db xref: HOM_0000065

RO HOM0000066
textual definition: Biological homology that involves parts of the same organism.
has_exact_synonym: iterative homologous to

Axiom
annotated source: RO HOM0000066
annotated property: textual definition
annotated target: Biological homology that involves parts of the same organism.
has db xref: annurev.es.20.110189.000411
has db xref: HOM_0000066

RO HOM0000068
textual definition: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
has_exact_synonym: duplicate xenology
has_exact_synonym: multiple xenology
has_exact_synonym: paraxenologous to

Axiom
annotated source: RO HOM0000068
annotated property: textual definition
annotated target: Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.
has db xref: HOM_0000068
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/3065587

RO HOM0000069
textual definition: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
has_exact_synonym: plerologous to

Axiom
annotated source: RO HOM0000069
annotated property: textual definition
annotated target: Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.
has db xref: HOM_0000069
has db xref: http://www.ncbi.nlm.nih.gov/pubmed/3065587

RO HOM0000071
textual definition: Structural homology that involves structures with the same or similar relative positions.
has_exact_synonym: homotopous to

Axiom
annotated source: RO HOM0000071
annotated property: textual definition
annotated target: Structural homology that involves structures with the same or similar relative positions.
has db xref: http://dx.doi.org/10.1007/BF02814484
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: HOM_0000071
has db xref: ISBN:0123195837

RO HOM0000072
textual definition: Biological homology that involves an ectopic structure and the normally positioned structure.
has_related_synonym: heterotopy

Axiom
annotated source: RO HOM0000072
annotated property: textual definition
annotated target: Biological homology that involves an ectopic structure and the normally positioned structure.
has db xref: http://dx.doi.org/10.1007/BF02814485
has db xref: j.cell.2008.06.030
has db xref: HOM_0000072

RO HOM0000073
textual definition: Synology that results from allopolyploidy.
has_exact_synonym: homoeologous to

Axiom
annotated source: RO HOM0000073
annotated property: textual definition
annotated target: Synology that results from allopolyploidy.
has db xref: pnas.0505156102
has db xref: HOM_0000073

RO HOM0000074
textual definition: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
has_related_synonym: axis paramorphism

Axiom
annotated source: RO HOM0000074
annotated property: textual definition
annotated target: Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.
has db xref: s10441-007-9023-8
has db xref: j.1525-142x.2000.00054.x
has db xref: HOM_0000074

RO HOM0000075
textual definition: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
has_exact_synonym: regulogous to

Axiom
annotated source: RO HOM0000075
annotated property: textual definition
annotated target: Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.
has db xref: gr.1774904
has db xref: HOM_0000075

UBERON_0000122
textual definition: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
has_exact_synonym: funiculus
has_exact_synonym: nerve fiber bundle
has_exact_synonym: neural fiber bundle

Axiom
annotated source: UBERON_0000122
annotated property: textual definition
annotated target: A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
has db xref: CARO:0001001
has db xref: FBC:DOS
has db xref: FBbt:00005099

Axiom
annotated source: UBERON_0000122
annotated property: has_exact_synonym
annotated target: nerve fiber bundle
has db xref: FBbt:00005099

UBERON_0000466
textual definition: Anatomical entity that has no mass.
has_exact_synonym: immaterial physical anatomical entity

Axiom
annotated source: UBERON_0000466
annotated property: textual definition
annotated target: Anatomical entity that has no mass.
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: UBERON_0000466
annotated property: has_exact_synonym
annotated target: immaterial physical anatomical entity
has db xref: FMA:67112

UBERON_0001062
textual definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.

Axiom
annotated source: UBERON_0001062
annotated property: textual definition
annotated target: 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.
has db xref: FMA:62955
has db xref: http://orcid.org/0000-0001-9114-8737

UBERON_0001981
textual definition: A vessel through which blood circulates in the body.
editor note: consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
has_broad_synonym: vascular element
has_exact_synonym: region of vascular tree organ
has_exact_synonym: vascular tree organ region

Axiom
annotated source: UBERON_0001981
annotated property: textual definition
annotated target: A vessel through which blood circulates in the body.
has db xref: BTO:0001102
has db xref: Wikipedia:Blood_vessel

Axiom
annotated source: UBERON_0001981
annotated property: has_broad_synonym
annotated target: vascular element
has db xref: EMAPA:35993

Axiom
annotated source: UBERON_0001981
annotated property: has_exact_synonym
annotated target: region of vascular tree organ
has db xref: FMA:50722

Axiom
annotated source: UBERON_0001981
annotated property: has_exact_synonym
annotated target: vascular tree organ region
has db xref: FMA:50722

UBERON_0001982
textual definition: Any of the smallest blood vessels connecting arterioles with venules.
editor note: not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
has_exact_synonym: blood capillary
has_exact_synonym: capillary vessel

Axiom
annotated source: UBERON_0001982
annotated property: textual definition
annotated target: Any of the smallest blood vessels connecting arterioles with venules.
has db xref: ISBN:0073040584
has db xref: Wikipedia:Capillary
has db xref: https://github.com/obophenotype/uberon/issues/137

UBERON_0010000
textual definition: An anatomical structure that has more than one cell as a part.
has_exact_synonym: multicellular structure

Axiom
annotated source: UBERON_0010000
annotated property: textual definition
annotated target: An anatomical structure that has more than one cell as a part.
has db xref: CARO:0010000

Axiom
annotated source: UBERON_0010000
annotated property: has_exact_synonym
annotated target: multicellular structure
has db xref: FBbt:00100313