Giorgio A. Ubbiali 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/ 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. https://creativecommons.org/licenses/by/4.0/ L'ontologia fondazionale della sostenibilità L'ontologie fondationnelle de la durabilité Sustainability Core Ontology (SCO) Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr https://www.w3id.org/sco/sco-u https://www.w3id.org/sco/sco-u-b-mapping 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 2025-03-19 Version 1.1.0. ; segment B. 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. Repository: https://github.com/gioUbbiali/Sustainability-Core-Ontology Documentation webpage: https://www.w3id.org/sco/docs 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. 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. The most recent version of this file is available on GitHub at the following link: https://www.w3id.org/sco editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example of usage 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status 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. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note term editor 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 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label 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. PERSON:Daniel Schober OBO Operations committee GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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). alternative label definition source 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item expand expression to 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)" 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 Chris Mungall expand expression to elucidation person:Alan Ruttenberg Person:Barry Smith 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 elucidation 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. temporal interpretation 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 http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property contributor entity responsible for making contributions to the resource creator entity responsible for making the resource source related resource from which the described resource is derived 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. An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 adapted from source for the resource that was modified to create the subject resource direct source definitive source of the subject resource excerpted from source of a resource that was imported unmodified from an external ontology 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). explanatory note note that provides additional explanatory information about a given notion or resource first-order logic axiom logic axiom annotation written in first order logic 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. first order logic definition logic definition that expresses the axioms of a class or an object property in first order logic 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)) 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 - {,}. is primitive boolean flag indicating that necessary and sufficient conditions are not provided '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 logical statements constraining the interpretation of the notion represented by the construct that do not provide necessary and sufficient conditions 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. 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. logic definition definition in the form of a logical expression maturity annotation property used to indicate the development status of a resource 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 definition written in plain text for human understanding 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'. primitive rationale reason why necessary and sufficient conditions could not be provided 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. semi-formal natural language axiom logic axiom expressed in natural language 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. semi-formal natural language definition logic definition that expresses a first order logic definition or common logic definition in natural language 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. subject matter expert explanation 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 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 usage note note that provides information about how a given notion or resource is used in the ontology's context 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 on perspectives. This procedure, however, ensures the possibility to also account for different characterizations of the same entity according to different perspectives, thereby assisting in clarifying and comparing those perspectives. Further, as a user may change perspective over time, this procedure can be performed whenever the perspective changes. New classes, covering time references, can be created and annotated with new perspectives. This will also assist in tracking users’ perspectives evolution over time. We contemplate the possible creation of an object property to directly model grounding on perspectives as part of future implementations of SCO. according to the perspective secondo la prospettiva selon la perspective inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple 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. inheres_in 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. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of 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. bearer_of is bearer of has characteristic this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence 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. function_of is function of 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. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of 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 this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence 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. is role of role_of 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 this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence 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. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence 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. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence 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. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition 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. disposition of A is spatially_disjoint_from B if and only if they have no parts in common 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. 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 BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to depends on A primitive relationship between an Information Content Entity and some Entity. http://purl.obolibrary.org/obo/IAO_0000136 http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology is about A primitive relationship between an instance of an Entity and an instance of an Information Content Entity. http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology is subject of 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. http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology See notes for inverse property. represented by 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. 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. http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology 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. represents 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. 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. 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. 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. a un agent au temps t ha un agente al tempo t has agent at time t comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029 http://www.ontologyrepository.com/CommonCoreOntologies/agent_in http://www.ontologyrepository.com/CommonCoreOntologies/has_agent A primitive relation between a process x, a continuant y, and a time at which y is causally active in x. Una relazione primitiva tra un processo x, un continuante y e un tempo t a cui y è causalmente attivo in x. Une relation primitive entre un processus x, un continuant y et un temps t auquel y est causalement actif en x. https://doi.org/10.1186/gb-2005-6-5-r46 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. agent en au temps t agent in at time t agente in al tempo t comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029 See information under the inverse "has agent at t" property. A primitive relation between a continuant x, a process y, and a time at which x is causally active in y. Una relazione primitiva tra un continuante x, un processo y e un tempo t a cui x è causalmente attivo in y. Une relation primitive entre un continuant x, un processus y et un temps t auquel x est causalement actif en y. 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]) 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]) 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]) 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. 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]) An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 http://www.jbiomedsem.com/content/4/1/43 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). 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 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 system 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 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 comments to https://www.w3id.org/sco/sco-u#SCO_0000056 ICE A Generically Dependent Continuant that generically depends on some Information Bearing Entity and stands in relation of aboutness to some Entity. http://purl.obolibrary.org/obo/IAO_0000030 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. http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology 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 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. Information Content Entity An Information Content Entity that represents some Entity. the content of a court transcript represents a courtroom proceeding the content of a photograph of the Statue of Liberty represents the Statue of Liberty the content of a video of a sporting event represents that sporting event http://www.ontologyrepository.com/CommonCoreOntologies/Mid/InformationEntityOntology Representational Information Content Entity maturity level classifier used to specify the state of a resource in its development process 2 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.” interaction interaction interazione http://purl.obolibrary.org/obo/INO_0000015 http://purl.obolibrary.org/obo/INO_0000016 A process that has at least two independent continuants (no spatial regions) as participants that have an effect upon one another. Un processo che ha almeno due continuanti indipendenti (no regioni spaziali) come partecipanti, aventi un effetto l’una sull’altra. Un processus qui a au moins deux continuants indépendants (pas de régions spatiales) comme participants, ayant un effet l’une sur l’autre. http://purl.obolibrary.org/obo/INO_0000002 This class has been restricted to those specific subclasses for the purposes of SCO. 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 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. développement de système sviluppo del sistema system development A process whose specific outcome is the progression of a system over time from an initial condition to a later condition. Un processo il cui specifico risultato è la progressione di un sistema nel tempo da una condizione iniziale a una condizione successiva. Un processus dont le résultat spécifique est la progression d’un système dans le temps, depuis une condition initiale à une condition suivante. http://purl.obolibrary.org/obo/GO_0032502 indicator information il valore dell'indicatore indicator value la valeur de l’indicateur See the comments under the corresponding "indicator" class. http://purl.unep.org/sdg/SDGIO_00000000 http://purl.unep.org/sdg/SDGIO_00000001 http://purl.unep.org/sdg/SDGIO_00000003 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. 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. Un contenuto informativo rappresentativo che genericamente dipende da un indicatore e riguarda, fornisce informazioni sul, sistema complesso a cui l'indicatore appartiene. 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 contenu informatif de la perspective contenuto informativo della prospettiva perspective information content entity 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. 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. 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. contenu informatif de la valeur contenuto informativo del valore worth information content entity 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. 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). 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). 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 context See the comment under the "system" class. 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 ambiente del sistema environnement de système system environment A material entity that surrounds and is distinct and disjoint from a system. Un'entità materiale che circonda ed è distinta e disgiunta da un sistema. Une entité matérielle qui entourne et qui est distincte et disjointe d’un système. 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 comments to https://www.w3id.org/sco/sco-u#SCO_0000056 2 relation among system components, interconnection among system components Interaction entre les composantes de système interaction among system components interazione tra le componenti del sistema An interaction that occurs among at least two system components. Une interaction qui se produit entre au moins deux composantes de système. Un’interazione che avviene tra almeno due componenti del sistema. 2 relation among system environment components, interconnection among system environment components interaction among system environment components interaction entre les composantes de l’environnement de système interazione tra le componenti dell’ambiente di sistema An interaction that occurs among at least two system environment components. Une interaction qui se produit entre au moins deux composantes de l’environnement d’un système. Un’interazione che avviene tra almeno due componenti dell’ambiente di un sistema. relation between system components and the system environment, interconnection between system components and the system environment Interaction entre les composantes de système et les composantes de l’environnement de système interaction between system components and system environment components interazione tra le componenti del sistema e le componenti de l'ambiente del sistema 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. 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. 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. complex system development développement de système complexe sviluppo del sistema complesso Le développement d’un système complexe. Lo sviluppo di un sistema complesso. The system development of a complex system. historie de système storia del sistema system history La storia di un sistema. L’histoire d’un système. The history of a system. complex system context ambiente del sistema complesso complex system environment environnement de système complexe A system environment that surrounds and is distinct and disjoint from a complex system. Un ambiente del sistema che circonda ed è distinto e disgiunto da un sistema complesso. Un environnement de système qui entourne et qui est distinct et disjoint d’un système complexe. system element system variable 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 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 componente del sistema composante de système system component A material entity that belongs to a system. Un'entità materiale che appartiene a un sistema. Une entité matérielle qui appartient à un système. 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 comments to https://www.w3id.org/sco/sco-u#SCO_0000056 system environment element system environment variable 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 componente dell' ambiente del systema composante de l'environnement de système system environment component A material entity that belongs to a system environment. Un'entità materiale che appartiene all’ambiente di un sistema. Une entité matérielle qui appartient à l’environnement d’un système. 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 comments to https://www.w3id.org/sco/sco-u#SCO_0000056 Ubbiali, G. A., Borghini, A., & Lange, M. C. (2024). Ontologies for Sustainability: Theoretical Challenges. https://doi.org/10.31219/osf.io/z8uqr socio-ecological system, social-ecological system complex system sistema complesso système complexe 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 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. 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. 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. 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. perspective perspective prospettiva 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. 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. 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. 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. indicateur (rôle) indicator-role ruolo di indicatore See the comments under the corresponding "indicator" class. 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. 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. 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. ruolo di parte interessata (stakeholder) rôle de partie prenante (stakeholder) stakeholder-role 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). 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). 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). value 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). 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. Valeur (sens donner de la valeur) valore (senso dare valore) worth-role (related) http://humanbehaviourchange.org/ontology/BCIO_006063 https://bio.scai.fraunhofer.de/ontology/epilepsy#worthiness 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. 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. 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. relation between complex system components and complex system environment components, interconnection between complex system components and complex system environment components Interaction entre les composantes de système complexe et les composantes de environnement de système complexe interaction between complex system components and complex system environment components interazione tra le componenti del sistema complesso e le componenti dell’ambiente del sistema complesso 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. 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. 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. 2 relation among complex system environment components, interconnection among complex system environment components interaction among complex system environment components interaction entre les composants de l’environnement de système complexe interazione tra le componenti dell’ambiente di sistema complesso An interaction that occurs among at least two complex system environment components. Une interaction qui se produit entre au moins deux composantes de l’environnement d’un système complexe. Un’interazione che avviene tra almeno due componenti dell’ambiente di un sistema complesso. 2 relation among complex system components, interconnection among complex system components Interaction entre les composantes de système complexe interaction among complex system components interazione tra le componenti del sistema complesso An interaction that occurs among at least two system components of a complex system. Une interaction qui se produit entre au moins deux composantes de système d’un système complexe. Un’interazione che avviene tra almeno due componenti del sistema di un sistema complesso. complex system history historie de système complexe storia del sistema complesso La storia del sistema di un sistema complesso. L’historique de système d’un système complexe. The system history of a complex system. Future SCO implementations may deal with representing system environment boudaries. confine del sistema frontière de système system boundary A fiat surface of a system. Una superficie fiat di un sistema. Une surface fiat d’un système. Future SCO implementations may consider including classes also covering spatial region for the system environment. regione spaziale del sistema région d’espace de système system spatial region A three-dimensional spatial region of a system. Una regione di spazio tridimensionale di un sistema. Une région d’espace tridimensionnelle d’un système. complex system environment element complex system environment variable complex system environment component componente dell' ambiente del systema complesso composante de l'environnement de système complexe A system evironment component that belongs to the system environment of a complex system. Una componente dell'ambiente di sistema che appartiene all’ambiente di un sistema complesso. Une composante de l'environnement de système qui appartient à l’environnement d’un système complexe. 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. agent de l’environnement de système agente dell’ambiente del sistema system environnement agent comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029 See information under the "has agent at t" property. 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. 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. 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. complex system element complex system variable complex system component componente del sistema complesso composante de système complexe A system component that belongs to a complex system. Una componente del sistema che appartiene a un sistema complesso. Une composante de système qui appartient à un système complexe. 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. agent de système agente del sistema system agent comments to https://www.w3id.org/sco/sco-u#SCO_0000027 and https://www.w3id.org/sco/sco-u#SCO_0000029 See information under the "has agent at t" property. A system component that is an agent in an interaction among system components or in an interaction between system components and system environment components. 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. 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. complex system stakeholder perspective, system stakeholder perspective Prospettiva di parte interessata (stakeholder) perspective de partie prenante (stakeholder) stakeholder perspective A perspective that is bearered by a stakeholder. Una prospettiva che è detenuta da una parte interessata (stakeholder). Une perspective qui est détenue par une partie prenante (stakeholder). complex system boundary confine del sistema complesso frontière de système complexe A system boundary of a complex system. Un confine del sistema di un sistema complesso. Une frontière de système d’un système complexe. complex system spatial region regione spaziale del sistema complesso région d’espace de système complexe A system spatial region of a complex system. Una regione di spazio del sistema di un sistema complesso. Une région d’espace de système d’un système complexe. agent de l’environnement de système complexe agente dell’ambiente del sistema complesso complex system environment agent See information under the "has agent at t" property. 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. 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. 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. agent de système complexe agente del sistema complesso complex system agent See information under the "has agent at t" property. 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. 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. 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. complex system indicator system indicator 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. 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. indicateur indicator indicatore http://purl.unep.org/sdg/SDGIO_00000002 A complex system component with an indicator role. Una componente del sistema complesso con un ruolo d’indicatore. Une composante de système complexe ayant un rôle d’indicateur. complex system stakeholder, system stakeholder parte interessata (stakeholder) partie prenante (stakeholder) stakeholder A complex system component with a stakeholder role. Una componente del sistema complesso con un ruolo di stakeholder. Une composante du système complexe avec un rôle de partie prenante. contenu informatif de la perspective de partie prenante (stakeholder) contenuto informativo della prospettiva di parte interessata (stakeholder) stakeholder perspective information content entity A perspective information content entity of a stakeholder perspective. Un contenu informatif de la perspective d’une perspective de partie prenante (stakeholder). Un contenuto informativo della prospettiva di una prospettiva di parte interessata (stakeholder). 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. complex system property proprietà del systema complesso propriété de système complexe 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 This class should be amended according to SCO implementations regarding system scales, levels, and change. emergence emergenza (proprietà emergenti) émergence (propriété émergentes 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. 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. 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. This class should be amended according to SCO implementations regarding system scales, levels, and change. auto-organisation auto-organizzazione self-organization 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. 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. 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. provisional construct or ontology development state in which content is subject to change and may change considerably IOF users should be aware that the resource is not dependable, but can be used for reference and for further work. released construct or ontology development state in which the resource is stable, usable, and has been made available to external users 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. 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. An entity that has temporal parts and that happens, unfolds or develops through time. 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. is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole 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. 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/ 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'. part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part 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. 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/ 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'. has_part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [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]) realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility 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]) preceded by 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. 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. is preceded by preceded_by precedes 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. 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 occurs_in unfolds in unfolds_in site of [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 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. A material entity that has a plasma membrane and results from cellular division. 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. CARO:mah Any neuron having a sensory function; an afferent neuron conveying sensory impulses. Any neuron having a sensory function; an afferent neuron conveying sensory impulses. ISBN:0721662544 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. nerve cell 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. MESH:D009474 http://en.wikipedia.org/wiki/Neuron A process during which an organism comes into contact with another entity. A system which has the disposition to environ one or more material entities. environment A system which has the disposition to environ one or more material entities. DOI:10.1186/2041-1480-4-43 An environmental system which can sustain and allow the growth of an ecological population. An environmental system which can sustain and allow the growth of an ecological population. EnvO:EnvO 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. 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. molecular function 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. GOC:pdt 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. E2 E3 ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity ubiquitin protein-ligase activity ubiquitin-conjugating enzyme activity 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. GOC:BioGRID GOC:jh2 PMID:9635407 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. cell nucleus horsetail nucleus 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. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 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. A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. biological process physiological process single organism process single-organism process 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. GOC:pdt Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. phosphokinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. GOC:ai example to be eventually removed data item information content entity curation status specification 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. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. pending final vetting 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. Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification 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. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term split 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. has obsolescence reason 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. PERSON:Alan Ruttenberg PERSON:Melanie Courtot ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg denotator type 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. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters universal 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. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "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. Alan Ruttenberg named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. 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 Alan Ruttenberg to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI expand assertion to 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)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall first order logic expression 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. PERSON:Alan Ruttenberg antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg requires discussion 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. Alan Ruttenberg group:OBI OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. 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 . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> has ID digit count 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" 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) Person:Alan Ruttenberg has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 Person:Alan Ruttenberg has ID policy for 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" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID prefix 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" 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. Person:Alan Ruttenberg has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax is allocated id range 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" PERSON:Alan Ruttenberg has ontology root term 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. Nicolas Matentzoglu may be identical to 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. David Osumi-Sutherland scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg 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 term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg ontology module 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. ontology file base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. editors ontology module 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. source ontology module main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology curation subset ontology module 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. analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. single layer ontology module 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. ribbon subset exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. taxonomic bridge ontology module ontology module subsetted by expressivity obo basic subset ontology module 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 ontology module subsetted by OWL profile EL++ ontology module planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. '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.) 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. Bjoern Peters branch derived processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 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. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived container A device that can be used to restrict the location of material entities over time 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?) PERSON: Bjoern Peters device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 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 role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. organism animal fungus plant virus 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. 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') 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. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. 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. This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call '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 . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms A synonym type for describing ambiguous synonyms A synonym type for describing dubious synonyms EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants A synonym type for common misspellings A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway 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. A synonym type for names that have been used as primary labels in the past. The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A branchiness quality inhering in a bearer by virtue of the bearer's having branches. ramified ramiform A branchiness quality inhering in a bearer by virtue of the bearer's having branches. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. ISBN:0881923214 A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. proportion proportionality quotient ratio rate A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. PATOC:nw A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATOC:GVG participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process 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. has_participant 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). 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). 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. 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). 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). 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. OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. 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. 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. this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) 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 This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) 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 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'. derives_into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location 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/ location_of contained in 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): Containment is location not involving parthood, and arises only where some immaterial continuant is involved. contained_in contains penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) 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. 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. penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) 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. 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. ## Elucidation This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; ## How to interpret (informal) First the &quot;atemporal&quot; 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 ## 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) the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of surface of May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary A relation that holds between two neurons that are electrically coupled via gap junctions. The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). 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 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. Note from NCEAS meeting: consider changing primary label 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. 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). regulates in other organism A relationship that holds between a process that regulates a transport process and the entity transported by that process. A part of relation that applies only between occurrents. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. PMID:24138933 Wikipedia:Infant_mortality David Osumi-Sutherland <= 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. David Osumi-Sutherland David Osumi-Sutherland David Osumi-Sutherland di David Osumi-Sutherland David Osumi-Sutherland starts_at_end_of David Osumi-Sutherland David Osumi-Sutherland David Osumi-Sutherland ends_at_start_of meets David Osumi-Sutherland io David Osumi-Sutherland d during David Osumi-Sutherland o overlaps Relation between a neuron and a material anatomical entity that its soma is part of. relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] 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. A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. A relation between a motor neuron and a muscle that it synapses to via a type II bouton. Relation between a muscle and a motor neuron that synapses to it via a type II bouton. Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapsed in has neurotransmitter Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in A relation between a motor neuron and a muscle that it synapses to via a type III bouton. Relation between a muscle and a motor neuron that synapses to it via a type III bouton. Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. 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. has synapse in x overlaps y if and only if there exists some z such that x has part z and z part of y The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. has fasciculating component 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. X continuous_with Y if and only if X and Y share a fiat boundary. connected to 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 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 proper overlaps 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. ancestral_stucture_of evolutionarily_descended_from inverse of derived by descent from 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. lactation SubClassOf 'only in taxon' some 'Mammalia' 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. 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 tooth SubClassOf 'never in taxon' value 'Aves' 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. 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. a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). 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 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. non-overlapping with shares no parts with 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. 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] S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. 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 The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). 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. 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. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. 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 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. 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 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. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. 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). inverse of has phenotype 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 inverse of develops from 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" 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. every HOTAIR lncRNA is the gene product of some HOXC gene every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene 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 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' 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 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. FBbt has developmental precursor A parasite that kills or sterilizes its host inverse of parasitoid of inverse of directly develops from developmental precursor of 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. GO false p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') 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. 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) TODO: add homeomorphy axiom 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. mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' 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. has function realized in 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. has function in OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role agent in OBSOLETE x has participant y if and only if x realizes some active role that inheres in y has agent 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 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. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. 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. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO 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. inverse of surrounded by inverse of starts with Chris Mungall Allen Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor 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. Chris Mungall started by 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 x develops_in y if x is located in y whilst x is developing EHDAA2 Jonathan Bard, EHDAA2 A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. inverse of ends with Chris Mungall 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. Chris Mungall finished by 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 starts with process that occurs in 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 ends with process that occurs in 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. consumes 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. produces A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) 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. X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. 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. ExO:0000001 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. ExO:0000000 A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 A broad relationship between an exposure event or process and the course takes from the source to the target. http://purl.obolibrary.org/obo/ExO_0000004 Any relationship between an exposure event or process and any other entity. g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. Any portion of roundup 'has active ingredient' some glyphosate 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 active substance has active pharmaceutical ingredient inverse of has active ingredient 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. 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. inverse of connecting branch of Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y inverse of has developmental contribution from 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 induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 Inverse of developmentally induced by 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 false c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) 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. 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. A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. 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. affects 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 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 replaces Inverse of developmentally preceded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x 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. 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. inverse of ubiquiotously expressed in 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). 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. every flower development (GO:0009908) results in development of some flower (PO:0009046) 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. http://www.geneontology.org/GO.doc.development.shtml every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) 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. GOC:mtg_berkeley_2013 tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) 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. 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. GOC:mtg_berkeley_2013 bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) 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 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. GOC:mtg_berkeley_2013 foramen ovale closure SubClassOf results in disappearance of foramen ovale every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) Inverse of 'is substance that treats' 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 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. adapted for living in 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. 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. 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. 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. 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, 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. 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. 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. regulates localization of 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. 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 GOC:mtg_berkeley_2013 A relationship that holds via some environmental process A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 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. adapted for A relationship that holds between entities participating in some developmental process (GO:0032502) 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) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. 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. 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. 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 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. a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. this relation holds between c and p when c is part of some c', and c' is capable of p. false 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. c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c inverse of enables inverse of regulates inverse of negatively regulates inverse of positively regulates A relationship that holds via some process of localization 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. 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. 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. 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 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. 'pollen tube growth' results_in growth_of some 'pollen tube' 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) 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. 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. 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. 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. An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO has member is a mereological relation between a collection and an item. SIO inverse of has input inverse of has output 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. 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. 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. 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 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. Wikipedia:Insertion_(anatomy) 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. Wikipedia:Insertion_(anatomy) false 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 has fused element 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. Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein 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. drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm Deschutes River distributary_of Little Lava Lake 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 branch of distributary channel of http://en.wikipedia.org/wiki/Distributary 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. anastomoses with A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location 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 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 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'. 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. x proper_distributary_of y iff x distributary_of y and x does not flow back into y x proper_tributary_of y iff x tributary_of y and x does not originate from y 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). x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y 'protein catabolic process' SubClassOf has_direct_input some protein 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. directly consumes translation SubClassOf has_direct_output some protein 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. directly produces inverse of upstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits 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. 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 yield a cross-product of different relation types. 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. https://en.wikipedia.org/wiki/Causality 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. 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. 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. directly provides input for transitive form of directly_provides_input_for 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. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects 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. A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL false inverse of causally upstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p c involved in regulation of p if c is involved in some p' and p' positively regulates some p c involved in regulation of p if c is involved in some p' and p' negatively regulates some p 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 OWL does not allow defining object properties via a Union involved in or reguates A protein that enables activity in a cytosol. 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. executes activity in enables activity in 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. 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. A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' 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. in pairwise interaction with An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) 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. binds molecularly binds with 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. interacts with on organism level An interaction relationship in which the partners are related via a feeding relationship. A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill 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 is subject of predation interaction with preys upon A biotic interaction in which the two organisms live together in more or less intimate association. http://www.ncbi.nlm.nih.gov/pubmed/19278549 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). http://www.ncbi.nlm.nih.gov/pubmed/19278549 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). http://www.ncbi.nlm.nih.gov/pubmed/19278549 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). http://www.ncbi.nlm.nih.gov/pubmed/19278549 Pediculus humanus capitis parasite of human A parasite-host relationship where an organism benefits at the expense of another. parasitizes direct parasite of Inverse of parasite of has parasite parasitised by directly parasitized by Porifiera attaches to substrate 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. semibiotically interacts with Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. 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. molecularly controls 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. directly inhibits molecularly decreases activity of 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. directly activates molecularly increases activity of all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints A relation that holds between a disease or an organism and a phenotype 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 Bees pollinate Flowers 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. is subject of pollination interaction with has polinator is target of pollination interaction with Inverse of provides nutrients for inverse of preys on has predator is target of predation interaction with Anopheles is a vector for Plasmodium a is a vector for b if a carries and transmits an infectious pathogen b into another living organism A biotic interaction where a material entity provides nutrition for an organism. A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. is subject of eating interaction with Inverse of eats eaten by is target of eating interaction with 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. 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' 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. 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. 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. shares no connection with ABal nucleus child nucleus of ABa nucleus (in C elegans) 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 A child nucleus relationship in which the cells are part of a hermaphroditic organism A child nucleus relationship in which the cells are part of a male organism 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. An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later 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) See notes for inverse relation 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. 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). 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). 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)) 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) exists during 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). 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). x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships 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 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). 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. A relationship between a material entity and a process where the material entity has some causal role that influences the process 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. 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 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. brain always_present_in_taxon 'Vertebrata' forelimb always_present_in_taxon Euarchontoglires S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S 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. never lost in 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c has intermediate product 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 A coral reef environment is determined by a particular coral reef 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. 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 inverse of determined by 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. x is transcribed from y if and only if x is synthesized from template y http://www.ncbi.nlm.nih.gov/pubmed/20226267 inverse of transcribed from http://www.ncbi.nlm.nih.gov/pubmed/20226267 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 http://www.ncbi.nlm.nih.gov/pubmed/20226267 inverse of ribosomal translation of http://www.ncbi.nlm.nih.gov/pubmed/20226267 A relation that holds between two entities that have the property of being sequences or having sequences. http://www.ncbi.nlm.nih.gov/pubmed/20226267 Every UTR is adjacent to a CDS of the same transcript Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent 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 http://www.ncbi.nlm.nih.gov/pubmed/20226267 Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 inverse of has start sequence starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 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) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 inverse of has end sequence ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 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. In the SO paper, this was defined as an instance-type relation http://www.ncbi.nlm.nih.gov/pubmed/20226267 Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. 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 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) 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 inverse of bounds sequence of x has subsequence y iff all of the sequence parts of y are sequence parts of x contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 inverse of has subsequence contained by x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. 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. disconnected from inverse of downstream of sequence of 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. A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript 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 A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of Any entity that is ordered in discrete units along a linear axis. Any individual unit of a collection of like units arranged in a linear order Any entity that can be divided into parts such that each part is an atomical unit of a sequence 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. 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. 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. 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 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. 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 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. 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 Count of number of days intervening between the start of the stage and the time of coitum. Count of number of days intervening between the end of the stage and the time of coitum. Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' 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. has supporting framework 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. x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y 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 http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite hyperparasitoid of epiparasite of inverse of hyperparasite of has epiparasite has hyperparasite hyperparasitoidized by http://en.wikipedia.org/wiki/Allelopathy Inverse of has pathogen A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member inverse of is evidence for 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 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 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 Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c 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). A relation that holds between elements of a musculoskeletal system or its analogs. 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. Wikipedia:Antagonist_(muscle) inverse of branching part of 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. UBERON:cjm 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. s is luminal space of x iff s is lumen_of x and s is an immaterial entity A relation that holds between an attribute or a qualifier and another attribute. 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 The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" inverse of has skeleton p directly regulates q iff p is immediately causally upstream of q and p regulates q. 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 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 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. 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). gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' 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 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. 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 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. p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c 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). 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. 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. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. pazopanib -> pathological angiogenesis 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. treats treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship benzene -> cancer [CHEBI] 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. causes disease A shortcut relationship that holds between two entities based on their identity criteria 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. x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' 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). 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). 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. treats 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. May be ceded to OBI Inverse of 'causal agent in process' 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. 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. A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. Inverse of is-model-of 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. 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. https://github.com/jhpoelen/eol-globi-data/issues/143 p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host inverse of ectoparasite of A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system lives inside of A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite inverse of mesoparasite of A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. inverse of intercellular endoparasite of A sub-relation of endoparasite-of in which the parasite inhabits host cells. inverse of intracellular endoparasite of 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. 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. 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. 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. inverse of reservoir host of 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. a produced_by b iff some process that occurs_in b has_output a. 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. 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. 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. is used to study 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'. 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. 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'. 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. 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. 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. contributes to expressivity of condition 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. contributes to penetrance of condition 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. is preventative for condition A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. 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. 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. 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. p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 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]. 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]. 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]. 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]. 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]. Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. 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. A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. 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. A relationship between a disease and a process where the disease process disrupts the execution of the process. A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology 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 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. A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. 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. Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 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 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 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. Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" 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. 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. An interaction relationship wherein a plant or algae is living on the outside surface of another plant. https://en.wikipedia.org/wiki/Epiphyte inverse of epiphyte of A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material https://en.wikipedia.org/wiki/Kleptoparasitism inverse of kleptoparasite of An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. 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. inverse of lays eggs on Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. muffin 'has substance added' some 'baking soda' "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. 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. 'egg white' 'has substance removed' some 'egg yolk' "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. sardines 'immersed in' some 'oil and mustard' "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. sardine has consumer some homo sapiens '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. bread 'has primary substance added' some 'flour' '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. 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. A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. Inverse of 'assay measures characteristic' A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. 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) 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. 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. triggered by process triggered by process Genetic information generically depend on molecules of DNA. The novel *War and Peace* generically depends on this copy of the novel. The pattern shared by chess boards generically depends on any chess board. The score of a symphony g-depends on a copy of the score. This pdf file generically depends on this server. 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*. [072-ISO] g-depends on Molecules of DNA are carriers of genetic information. This copy of *War and Peace* is carrier of the novel written by Tolstoy. This hard drive is carrier of these data items. *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* [072-ISO] 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. The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. 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. 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. The entity A has an activity that directly positively regulates the quantity of B. The entity A has an activity that directly negatively regulates the quantity of B. The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. indirectly activates AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. indirectly inhibits The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. 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. 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. 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. a relation between a process and a continuant, in which the process is regulated by the small molecule continuant a relation between a process and a continuant, in which the process is activated by the small molecule continuant a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant p acts on population of c iff c' is a collection, has members of type c, and p has participant c a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process a relation between a continuant and a process, in which the continuant is a small molecule that activates the process a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process 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. 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. 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. 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. p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 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). positively regulates in other organism 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). negatively regulates in other organism 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 synaptic input or output in A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. 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). 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). 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). Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. has sensory dendrite location has sensory terminal in has sensory terminal location A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) A relation between a material entity and some data in which the data is taken as exemplifying the material entity. 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. A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. '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'). 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. A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. 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 marker gene combination has marker signature set 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 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. 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. https://orcid.org/0000-0002-6601-2165 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') 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. 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. PMID:19243617 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') 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. 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. PMID:19243617 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. 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. ExO:0000083 A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. utilizes A relation between entities in which one increases or decreases as the other does the same. directly correlated with A relation between entities in which one increases as the other decreases. inversely correlated with anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. A relation between a container and measurement datum that specifies the actual amount of material in the container. anticoagulant-containing test tube has maximum capacity 10 ml. 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. biobank organization owns a specimen hospital owns a laboratory facility A primitive relation that holds between entities x and y in which y is at x's full disposal. freezer is owned by a biobank organization Inverse of the owns relation. Helper relation for OWL definition of RO:0018002 myristoylates A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input inverse of myristoylates mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) 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 pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) 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 tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) 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 pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) 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. neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) 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. (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. 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. (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. 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. 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. 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. is MMP with is matched molecular pair with 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. 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. 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. is desmotrope of 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. carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) 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. carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) 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. hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. 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). is optical isomer of dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. 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. 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. 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. 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. 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. 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. Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. brachial artery vessel supplies blood to brachialis muscle 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. cystic vein vessel drains blood from gallbladder 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. alveolar capillary directly supplies and drains some alveolus 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. A relationship between a ratio or proportion and its dividend. has dividend A relationship between a ratio or proportion and its divisor. has divisor This relation groups relations between diseases and any other kind of entity. p has anatomical participant c iff p has participant c, and c is an anatomical entity part-of is homeomorphic for independent continuants. 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. Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom sameness similar to correspondence resemblance Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. BGEE:curator correspondence Similarity that results from common evolutionary origin. homologous to Similarity that results from common evolutionary origin. Similarity that results from independent evolution. homoplasous to analogy Similarity that results from independent evolution. Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. homocracous to Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. Homoplasy that involves different underlying mechanisms or structures. analogy Homoplasy that involves different underlying mechanisms or structures. Homoplasy that involves homologous underlying mechanisms or structures. parallel evolution Homoplasy that involves homologous underlying mechanisms or structures. Homology that is defined by similarity with regard to selected structural parameters. structural homologous to idealistic homology Homology that is defined by similarity with regard to selected structural parameters. ISBN:0123195837 Homology that is defined by common descent. homology cladistic homology historical homologous to phylogenetic homology taxic homology true homology Homology that is defined by common descent. ISBN:0123195837 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. biological homologous to transformational homology 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. Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. atavism rudiment reversion Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. Structural homology that is detected by similarity in content and organization between chromosomes. syntenic homologous to synteny Structural homology that is detected by similarity in content and organization between chromosomes. MeSH:Synteny Historical homology that involves genes that diverged after a duplication event. paralogous to Historical homology that involves genes that diverged after a duplication event. Paralogy that involves sets of syntenic blocks. syntenic paralogous to duplicon paralogon Paralogy that involves sets of syntenic blocks. DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y Syntenic homology that involves chromosomes of different species. syntenic orthologous to Syntenic homology that involves chromosomes of different species. Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. fractional homology partial homologous to segmental homology mixed homology modular homology partial correspondence percent homology Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. ISBN:0123195837 ISBN:978-0471984931 Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. protein structural homologous to Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. Structural homology that involves a pseudogenic feature and its functional ancestor. pseudogene non functional homologous to Structural homology that involves a pseudogenic feature and its functional ancestor. SO:non_functional_homolog_of Historical homology that involves genes that diverged after a speciation event. orthologous to Historical homology that involves genes that diverged after a speciation event. Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. xenologous to Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. Historical homology that involves two members sharing no other homologs in the lineages considered. 1 to 1 homologous to 1:1 homology one-to-one homology Historical homology that involves two members sharing no other homologs in the lineages considered. BGEE:curator Orthology that involves two genes that did not experience any duplication after the speciation event that created them. 1 to 1 orthologous to 1:1 orthology one-to-one orthology Orthology that involves two genes that did not experience any duplication after the speciation event that created them. Paralogy that results from a whole genome duplication event. ohnologous to homoeology Paralogy that results from a whole genome duplication event. Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. in-paralogous to inparalogy symparalogy Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. Paralogy that results from a duplication preceding a given speciation event. alloparalogy out-paralogous to outparalogy Paralogy that results from a duplication preceding a given speciation event. 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. pro-orthologous to 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. 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. semi-orthologous to 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. Iterative homology that involves structures arranged along the main body axis. serial homologous to homonomy Iterative homology that involves structures arranged along the main body axis. Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. heterochronous homologous to heterochrony Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. ISBN:978-0674639416 Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. juvenification pedomorphosis Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. ISBN:978-0674639416 Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. ISBN:978-0674639416 Paedomorphosis that is produced by a retardation of somatic development. juvenilization neotenous to Paedomorphosis that is produced by a retardation of somatic development. ISBN:978-0674639416 Convergence that results from co-evolution usually involving an evolutionary arms race. mimicrous to Convergence that results from co-evolution usually involving an evolutionary arms race. Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. 1 to many orthologous to 1:many orthology one-to-many orthology co-orthology many to 1 orthology Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. Historical homology that involves two members of a larger set of homologs. many to many homologous to many-to-many homology many:many homology Historical homology that involves two members of a larger set of homologs. 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. 1 to many homologous to one-to-many homology 1:many homology 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. BGEE:curator Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. apomorphous to synapomorphy Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. ISBN:978-0252068140 Historical homology that is based on distant shared ancestry. plesiomorphous to symplesiomorphy Historical homology that is based on distant shared ancestry. ISBN:978-0252068140 Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. deep genetic homology deep homologous to generative homology homoiology Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. 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. hemiplasous to 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. Historical homology that involves not recombining and subsequently differentiated sex chromosomes. gametologous to Historical homology that involves not recombining and subsequently differentiated sex chromosomes. Historical homology that involves the chromosomes able to pair (synapse) during meiosis. chromosomal homologous to Historical homology that involves the chromosomes able to pair (synapse) during meiosis. ISBN:0195307615 Orthology that involves two genes that experienced duplications more recent than the species split that created them. many to many orthologous to many-to-many orthology many:many orthology trans-orthology co-orthology trans-homology Orthology that involves two genes that experienced duplications more recent than the species split that created them. Paralogy that involves genes from the same species. within-species paralogous to Paralogy that involves genes from the same species. Paralogy that involves genes from different species. between-species paralogous to Paralogy that involves genes from different species. Paedomorphosis that is produced by delayed growth of immature structures into the adult form. post-displacement Paedomorphosis that is produced by delayed growth of immature structures into the adult form. Peramorphosis that is produced by a delay in the offset of development. Peramorphosis that is produced by a delay in the offset of development. ISBN:978-0674639416 Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. synologous to Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. Orthology that involves functional equivalent genes with retention of the ancestral function. isoorthologous to Orthology that involves functional equivalent genes with retention of the ancestral function. Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. tandem paralogous to iterative paralogy serial paralogy Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. ISBN:978-0878932665 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). apomorphic tendency cryptic homology latent homologous to underlying synapomorphy homoiology homoplastic tendency re-awakening 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). ISBN:0199141118 Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. generative homology syngenous to Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. 1:1 paralogy apparent 1:1 orthology apparent orthologous to pseudoorthology Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. pseudoparalogous to Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. Historical homology that involves functional equivalent genes with retention of the ancestral function. equivalogous to Historical homology that involves functional equivalent genes with retention of the ancestral function. Historical homology that involves orthologous pairs of interacting molecules in different organisms. interologous to Historical homology that involves orthologous pairs of interacting molecules in different organisms. Similarity that is characterized by interchangeability in function. functional similarity Similarity that is characterized by interchangeability in function. Biological homology that involves parts of the same organism. iterative homologous to Biological homology that involves parts of the same organism. 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. duplicate xenology multiple xenology paraxenologous to 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. Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. plerologous to Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. Structural homology that involves structures with the same or similar relative positions. homotopous to Structural homology that involves structures with the same or similar relative positions. ISBN:0123195837 Biological homology that involves an ectopic structure and the normally positioned structure. heterotopy Biological homology that involves an ectopic structure and the normally positioned structure. Synology that results from allopolyploidy. homoeologous to Synology that results from allopolyploidy. 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. axis paramorphism 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. Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. regulogous to Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. funiculus nerve fiber bundle neural fiber bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 nerve fiber bundle FBbt:00005099 Anatomical entity that has no mass. immaterial physical anatomical entity Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 immaterial physical anatomical entity FMA:67112 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. 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. FMA:62955 http://orcid.org/0000-0001-9114-8737 A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus vascular element region of vascular tree organ vascular tree organ region A vessel through which blood circulates in the body. BTO:0001102 Wikipedia:Blood_vessel vascular element EMAPA:35993 region of vascular tree organ FMA:50722 vascular tree organ region FMA:50722 Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element blood capillary capillary vessel Any of the smallest blood vessels connecting arterioles with venules. ISBN:0073040584 Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 An anatomical structure that has more than one cell as a part. multicellular structure An anatomical structure that has more than one cell as a part. CARO:0010000 multicellular structure FBbt:00100313